Starting phenix.real_space_refine on Fri Sep 11 19:37:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.cif Found real_map, /net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.map" model { file = "/net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6seg_10155/09_2026/6seg_10155.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 288 5.49 5 S 10 5.16 5 C 6471 2.51 5 N 2175 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11689 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" 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: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.69, per 1000 atoms: 0.23 Number of scatterers: 11689 At special positions: 0 Unit cell: (74.24, 120.32, 113.92, 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 10 16.00 P 288 15.00 O 2745 8.00 N 2175 7.00 C 6471 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: 0.89 Conformation dependent library (CDL) restraints added in 248.6 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 72.9% alpha, 2.7% beta 127 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.819A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.082A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.531A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.869A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.890A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.780A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.164A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.613A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.586A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.507A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.792A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.504A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.077A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.766A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.501A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.746A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.556A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.616A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.656A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.259A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.599A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.570A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.617A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.700A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.490A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.754A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.871A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.583A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 357 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.26 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: 1875 1.33 - 1.45: 4394 1.45 - 1.57: 5633 1.57 - 1.68: 576 1.68 - 1.80: 18 Bond restraints: 12496 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.03e+01 bond pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DA J 65 " pdb=" C2' DA J 65 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA J 16 " pdb=" O3' DA J 16 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 12491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 17746 2.75 - 5.49: 357 5.49 - 8.24: 18 8.24 - 10.98: 3 10.98 - 13.73: 1 Bond angle restraints: 18125 Sorted by residual: angle pdb=" O4' DG I 70 " pdb=" C4' DG I 70 " pdb=" C3' DG I 70 " ideal model delta sigma weight residual 106.00 102.25 3.75 6.00e-01 2.78e+00 3.90e+01 angle pdb=" O5' DT J -71 " pdb=" C5' DT J -71 " pdb=" C4' DT J -71 " ideal model delta sigma weight residual 109.40 114.36 -4.96 8.00e-01 1.56e+00 3.84e+01 angle pdb=" O4' DT I 55 " pdb=" C4' DT I 55 " pdb=" C3' DT I 55 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.09e+01 angle pdb=" O4' DA I -35 " pdb=" C1' DA I -35 " pdb=" N9 DA I -35 " ideal model delta sigma weight residual 108.00 104.19 3.81 7.00e-01 2.04e+00 2.96e+01 angle pdb=" O4' DG I -68 " pdb=" C1' DG I -68 " pdb=" N9 DG I -68 " ideal model delta sigma weight residual 108.00 111.77 -3.77 7.00e-01 2.04e+00 2.90e+01 ... (remaining 18120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5311 34.97 - 69.95: 1378 69.95 - 104.92: 18 104.92 - 139.89: 0 139.89 - 174.87: 1 Dihedral angle restraints: 6708 sinusoidal: 4618 harmonic: 2090 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 45.13 174.87 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1878 0.099 - 0.198: 172 0.198 - 0.298: 7 0.298 - 0.397: 1 0.397 - 0.496: 1 Chirality restraints: 2059 Sorted by residual: chirality pdb=" CG LEU D 45 " pdb=" CB LEU D 45 " pdb=" CD1 LEU D 45 " pdb=" CD2 LEU D 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU E 112 " pdb=" CB LEU E 112 " pdb=" CD1 LEU E 112 " pdb=" CD2 LEU E 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2056 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.035 2.00e-02 2.50e+03 2.01e-02 9.09e+00 pdb=" N1 DC I 69 " -0.044 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " 0.038 2.00e-02 2.50e+03 1.97e-02 8.70e+00 pdb=" N1 DC I 35 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 5 " -0.037 2.00e-02 2.50e+03 1.91e-02 8.24e+00 pdb=" N1 DC I 5 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DC I 5 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 5 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 5 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DC I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 5 " 0.005 2.00e-02 2.50e+03 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2588 2.81 - 3.33: 9223 3.33 - 3.85: 23485 3.85 - 4.38: 27726 4.38 - 4.90: 38845 Nonbonded interactions: 101867 Sorted by model distance: nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.338 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.345 2.496 ... (remaining 101862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 111) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.240 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.008 0.059 12496 Z= 0.652 Angle : 0.991 13.727 18125 Z= 0.819 Chirality : 0.060 0.496 2059 Planarity : 0.007 0.063 1283 Dihedral : 27.752 174.868 5364 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.23), residues: 712 helix: -2.21 (0.17), residues: 515 sheet: None (None), residues: 0 loop : -1.95 (0.34), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 42 TYR 0.022 0.003 TYR F 98 PHE 0.015 0.003 PHE A 84 TRP 0.005 0.001 TRP E 47 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.65 (12496) covalent geometry : angle 0.99129 / 0.82 (18125) hydrogen bonds : bond 0.10465 / 7.21 ( 686) hydrogen bonds : angle 4.48599 / 3.10 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.290 Fit side-chains REVERT: A 53 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8125 (tmmt) REVERT: B 44 LYS cc_start: 0.8659 (tttt) cc_final: 0.8038 (mptt) REVERT: B 79 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7482 (mtpp) REVERT: C 73 ASN cc_start: 0.8222 (t0) cc_final: 0.7834 (t0) REVERT: C 74 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7454 (mttp) REVERT: C 95 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7535 (ttmm) REVERT: D 37 TYR cc_start: 0.8839 (m-80) cc_final: 0.8451 (m-80) REVERT: D 59 MET cc_start: 0.7932 (tpp) cc_final: 0.7607 (tpt) REVERT: E 62 ILE cc_start: 0.8163 (mt) cc_final: 0.7951 (mt) REVERT: G 36 LYS cc_start: 0.8438 (mptt) cc_final: 0.8158 (mptt) REVERT: G 90 ASP cc_start: 0.7445 (t0) cc_final: 0.7199 (t0) REVERT: H 99 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7767 (mtm110) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1855 time to fit residues: 26.4592 Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138126 restraints weight = 13482.515| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 0.86 r_work: 0.3352 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12496 Z= 0.158 Angle : 0.722 7.288 18125 Z= 0.421 Chirality : 0.052 0.248 2059 Planarity : 0.005 0.051 1283 Dihedral : 30.911 171.031 3964 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.84 % Allowed : 8.54 % Favored : 90.62 % 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: -0.88 (0.28), residues: 712 helix: -0.09 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 11 TYR 0.014 0.002 TYR F 98 PHE 0.014 0.001 PHE E 67 TRP 0.005 0.001 TRP E 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (12496) covalent geometry : angle 0.72224 / 0.42 (18125) hydrogen bonds : bond 0.06444 / 4.30 ( 686) hydrogen bonds : angle 3.39915 / 2.41 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.312 Fit side-chains REVERT: A 122 PHE cc_start: 0.8818 (m-80) cc_final: 0.8515 (m-80) REVERT: B 44 LYS cc_start: 0.8885 (tttt) cc_final: 0.8047 (mptt) REVERT: B 79 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7481 (mtpp) REVERT: C 74 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7392 (mttp) REVERT: C 95 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7699 (ttmm) REVERT: E 62 ILE cc_start: 0.8514 (mt) cc_final: 0.8270 (mt) REVERT: G 24 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7981 (mm-40) REVERT: G 36 LYS cc_start: 0.8599 (mptt) cc_final: 0.8373 (mptt) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.1738 time to fit residues: 23.2058 Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 69 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.175775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128659 restraints weight = 13588.603| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.14 r_work: 0.3295 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12496 Z= 0.197 Angle : 0.683 6.296 18125 Z= 0.391 Chirality : 0.049 0.267 2059 Planarity : 0.005 0.045 1283 Dihedral : 31.432 170.086 3964 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.68 % Allowed : 9.72 % Favored : 88.61 % 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: -0.03 (0.30), residues: 712 helix: 0.56 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.012 0.002 TYR F 98 PHE 0.014 0.002 PHE E 67 TRP 0.007 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (12496) covalent geometry : angle 0.68284 / 0.39 (18125) hydrogen bonds : bond 0.05639 / 3.71 ( 686) hydrogen bonds : angle 3.08598 / 2.19 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.269 Fit side-chains REVERT: A 79 THR cc_start: 0.8464 (p) cc_final: 0.8214 (p) REVERT: B 44 LYS cc_start: 0.8920 (tttt) cc_final: 0.8076 (mptt) REVERT: C 35 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: C 74 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7453 (mttp) REVERT: D 59 MET cc_start: 0.8867 (tpp) cc_final: 0.8530 (tpt) REVERT: E 62 ILE cc_start: 0.8605 (mt) cc_final: 0.8353 (mt) REVERT: G 24 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7977 (mm-40) REVERT: G 36 LYS cc_start: 0.8661 (mptt) cc_final: 0.8387 (mptt) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1574 time to fit residues: 21.1738 Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 90 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 37 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134493 restraints weight = 13582.595| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.07 r_work: 0.3329 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12496 Z= 0.130 Angle : 0.594 5.708 18125 Z= 0.353 Chirality : 0.043 0.250 2059 Planarity : 0.004 0.034 1283 Dihedral : 31.306 172.083 3964 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.68 % Allowed : 11.39 % Favored : 86.93 % 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: 0.74 (0.30), residues: 712 helix: 1.16 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP A 86 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.13 (12496) covalent geometry : angle 0.59368 / 0.35 (18125) hydrogen bonds : bond 0.05019 / 3.35 ( 686) hydrogen bonds : angle 2.81495 / 2.01 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.279 Fit side-chains REVERT: A 79 THR cc_start: 0.8114 (p) cc_final: 0.7748 (p) REVERT: A 114 LEU cc_start: 0.8346 (mt) cc_final: 0.7956 (mp) REVERT: B 44 LYS cc_start: 0.8917 (tttt) cc_final: 0.8002 (mptt) REVERT: B 79 LYS cc_start: 0.8043 (mttp) cc_final: 0.7303 (mtpp) REVERT: C 92 GLU cc_start: 0.8050 (pm20) cc_final: 0.7781 (pm20) REVERT: E 62 ILE cc_start: 0.8550 (mt) cc_final: 0.8247 (mt) REVERT: F 91 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8482 (ttpp) REVERT: G 24 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7973 (mm-40) REVERT: G 74 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7733 (mmtt) REVERT: G 112 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5630 (pt0) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1553 time to fit residues: 20.6343 Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137285 restraints weight = 13575.975| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 0.86 r_work: 0.3437 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12496 Z= 0.171 Angle : 0.628 6.238 18125 Z= 0.363 Chirality : 0.045 0.262 2059 Planarity : 0.004 0.042 1283 Dihedral : 31.449 171.319 3964 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % Favored : 86.60 % 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: 0.85 (0.30), residues: 712 helix: 1.27 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.010 0.002 TYR C 57 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (12496) covalent geometry : angle 0.62809 / 0.36 (18125) hydrogen bonds : bond 0.05054 / 3.36 ( 686) hydrogen bonds : angle 2.86178 / 2.03 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.201 Fit side-chains REVERT: A 79 THR cc_start: 0.8067 (p) cc_final: 0.7706 (p) REVERT: A 114 LEU cc_start: 0.8423 (mt) cc_final: 0.8068 (mp) REVERT: B 44 LYS cc_start: 0.8911 (tttt) cc_final: 0.8048 (mptt) REVERT: B 79 LYS cc_start: 0.8219 (mttp) cc_final: 0.7503 (mtpp) REVERT: C 35 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: E 62 ILE cc_start: 0.8830 (mt) cc_final: 0.8591 (mt) REVERT: F 91 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8530 (ttpp) REVERT: G 74 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7797 (mmtt) REVERT: G 112 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5619 (pt0) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.1677 time to fit residues: 21.1986 Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 50.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136610 restraints weight = 13560.565| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.86 r_work: 0.3406 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12496 Z= 0.163 Angle : 0.615 5.958 18125 Z= 0.357 Chirality : 0.044 0.262 2059 Planarity : 0.004 0.038 1283 Dihedral : 31.460 171.723 3964 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.51 % Allowed : 11.89 % Favored : 86.60 % 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: 0.98 (0.30), residues: 712 helix: 1.37 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.010 0.002 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (12496) covalent geometry : angle 0.61464 / 0.36 (18125) hydrogen bonds : bond 0.04962 / 3.30 ( 686) hydrogen bonds : angle 2.82888 / 2.01 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.227 Fit side-chains REVERT: A 79 THR cc_start: 0.7997 (p) cc_final: 0.7628 (p) REVERT: A 114 LEU cc_start: 0.8381 (mt) cc_final: 0.8042 (mp) REVERT: B 44 LYS cc_start: 0.8913 (tttt) cc_final: 0.7988 (mptt) REVERT: B 79 LYS cc_start: 0.8181 (mttp) cc_final: 0.7431 (mtpp) REVERT: C 35 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: C 92 GLU cc_start: 0.7822 (pm20) cc_final: 0.7614 (pm20) REVERT: D 108 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7466 (mtpp) REVERT: F 91 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8493 (ttpp) REVERT: G 24 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8034 (mm-40) REVERT: G 74 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7687 (mmtt) REVERT: G 112 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5758 (pt0) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.1654 time to fit residues: 20.9129 Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.178379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131146 restraints weight = 13589.286| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.11 r_work: 0.3297 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12496 Z= 0.152 Angle : 0.607 5.833 18125 Z= 0.354 Chirality : 0.044 0.260 2059 Planarity : 0.004 0.039 1283 Dihedral : 31.451 171.909 3964 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.51 % Allowed : 12.73 % Favored : 85.76 % 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: 1.09 (0.30), residues: 712 helix: 1.46 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 11 TYR 0.009 0.001 TYR E 110 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12496) covalent geometry : angle 0.60715 / 0.35 (18125) hydrogen bonds : bond 0.04881 / 3.25 ( 686) hydrogen bonds : angle 2.80224 / 1.99 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.288 Fit side-chains REVERT: A 79 THR cc_start: 0.8042 (p) cc_final: 0.7669 (p) REVERT: A 114 LEU cc_start: 0.8394 (mt) cc_final: 0.8016 (mp) REVERT: B 44 LYS cc_start: 0.8937 (tttt) cc_final: 0.8088 (mptt) REVERT: B 79 LYS cc_start: 0.8192 (mttp) cc_final: 0.7445 (mtpp) REVERT: C 35 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: C 92 GLU cc_start: 0.7923 (pm20) cc_final: 0.7721 (pm20) REVERT: D 108 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7489 (mtpp) REVERT: F 91 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8526 (ttpp) REVERT: G 24 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7849 (mm-40) REVERT: G 74 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7614 (mmtt) REVERT: G 112 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5528 (pt0) outliers start: 9 outliers final: 8 residues processed: 95 average time/residue: 0.1738 time to fit residues: 21.3386 Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.183818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138734 restraints weight = 13487.792| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.86 r_work: 0.3345 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12496 Z= 0.129 Angle : 0.597 9.661 18125 Z= 0.350 Chirality : 0.043 0.258 2059 Planarity : 0.004 0.042 1283 Dihedral : 31.426 172.045 3964 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.34 % Allowed : 13.23 % Favored : 85.43 % 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: 1.32 (0.30), residues: 712 helix: 1.63 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 11 TYR 0.012 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (12496) covalent geometry : angle 0.59659 / 0.35 (18125) hydrogen bonds : bond 0.04799 / 3.20 ( 686) hydrogen bonds : angle 2.75384 / 1.96 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.256 Fit side-chains REVERT: A 79 THR cc_start: 0.7962 (p) cc_final: 0.7588 (p) REVERT: A 114 LEU cc_start: 0.8236 (mt) cc_final: 0.7878 (mp) REVERT: B 44 LYS cc_start: 0.8915 (tttt) cc_final: 0.7936 (mptt) REVERT: B 79 LYS cc_start: 0.8092 (mttp) cc_final: 0.7314 (mtpp) REVERT: C 35 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: C 92 GLU cc_start: 0.7875 (pm20) cc_final: 0.7647 (pm20) REVERT: D 108 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7429 (mtpp) REVERT: F 91 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8449 (ttpp) REVERT: G 24 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7799 (mm-40) REVERT: G 74 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7585 (mmtt) REVERT: G 112 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5537 (pt0) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1584 time to fit residues: 19.1194 Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.183197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138033 restraints weight = 13410.270| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.86 r_work: 0.3347 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12496 Z= 0.143 Angle : 0.593 8.141 18125 Z= 0.348 Chirality : 0.043 0.259 2059 Planarity : 0.004 0.042 1283 Dihedral : 31.393 172.192 3964 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.34 % Allowed : 13.23 % Favored : 85.43 % 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: 1.40 (0.30), residues: 712 helix: 1.67 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.013 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (12496) covalent geometry : angle 0.59321 / 0.35 (18125) hydrogen bonds : bond 0.04728 / 3.15 ( 686) hydrogen bonds : angle 2.72784 / 1.94 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.306 Fit side-chains REVERT: A 79 THR cc_start: 0.7727 (p) cc_final: 0.7342 (p) REVERT: A 114 LEU cc_start: 0.8319 (mt) cc_final: 0.7967 (mp) REVERT: B 44 LYS cc_start: 0.8922 (tttt) cc_final: 0.7939 (mttt) REVERT: C 35 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7553 (mtm-85) REVERT: C 92 GLU cc_start: 0.7876 (pm20) cc_final: 0.7666 (pm20) REVERT: F 91 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8470 (ttpp) REVERT: G 24 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7712 (mm-40) REVERT: G 74 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7601 (mmtt) REVERT: G 112 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5478 (pt0) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1455 time to fit residues: 17.6241 Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.183600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138423 restraints weight = 13535.005| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.87 r_work: 0.3426 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 12496 Z= 0.130 Angle : 0.591 12.653 18125 Z= 0.346 Chirality : 0.042 0.259 2059 Planarity : 0.004 0.037 1283 Dihedral : 31.383 172.627 3964 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.34 % Allowed : 13.23 % Favored : 85.43 % 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: 1.52 (0.31), residues: 712 helix: 1.76 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.013 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 TRP 0.004 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (12496) covalent geometry : angle 0.59064 / 0.35 (18125) hydrogen bonds : bond 0.04676 / 3.12 ( 686) hydrogen bonds : angle 2.69409 / 1.92 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.231 Fit side-chains REVERT: A 79 THR cc_start: 0.7759 (p) cc_final: 0.7377 (p) REVERT: A 114 LEU cc_start: 0.8345 (mt) cc_final: 0.8002 (mp) REVERT: B 44 LYS cc_start: 0.8932 (tttt) cc_final: 0.8008 (mptt) REVERT: C 35 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: C 92 GLU cc_start: 0.7861 (pm20) cc_final: 0.7651 (pm20) REVERT: F 91 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8495 (ttpp) REVERT: G 24 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7737 (mm-40) REVERT: G 74 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7618 (mmtt) REVERT: G 112 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5511 (pt0) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1616 time to fit residues: 19.3415 Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.184773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139824 restraints weight = 13540.539| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.86 r_work: 0.3355 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12496 Z= 0.132 Angle : 0.575 6.583 18125 Z= 0.341 Chirality : 0.042 0.256 2059 Planarity : 0.004 0.037 1283 Dihedral : 31.353 172.765 3964 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.34 % Allowed : 13.40 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.30), residues: 712 helix: 1.83 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.014 0.001 TYR D 40 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (12496) covalent geometry : angle 0.57516 / 0.34 (18125) hydrogen bonds : bond 0.04585 / 3.06 ( 686) hydrogen bonds : angle 2.66889 / 1.90 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.11 seconds wall clock time: 48 minutes 45.72 seconds (2925.72 seconds total)