Starting phenix.real_space_refine on Fri Sep 11 09:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4g_30077/09_2026/6m4g_30077.cif" } resolution = 2.8 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= -0.002 sd= 1.046 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 186 5.49 5 S 16 5.16 5 C 5087 2.51 5 N 1657 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 9010 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1924 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1888 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Restraints were copied for chains: E, F, G, H Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 9010 At special positions: 0 Unit cell: (80.08, 115.44, 115.44, 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 16 16.00 P 186 15.00 O 2064 8.00 N 1657 7.00 C 5087 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: 0.61 Conformation dependent library (CDL) restraints added in 147.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 75.9% alpha, 2.1% beta 66 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.584A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.690A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 78 removed outlier: 3.866A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 78 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.122A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.674A pdb=" N THR F 96 " --> pdb=" O THR C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 325 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.79 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: 1683 1.33 - 1.45: 3039 1.45 - 1.57: 4417 1.57 - 1.68: 372 1.68 - 1.80: 28 Bond restraints: 9539 Sorted by residual: bond pdb=" C3' DG I 38 " pdb=" C2' DG I 38 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.89e+01 bond pdb=" C3' DG I 92 " pdb=" C2' DG I 92 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 1.99e+01 bond pdb=" C3' DC J 64 " pdb=" C2' DC J 64 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.82e+01 bond pdb=" C3' DT J 115 " pdb=" C2' DT J 115 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.74e+01 bond pdb=" C3' DA I 61 " pdb=" C2' DA I 61 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.69e+01 ... (remaining 9534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11902 1.43 - 2.86: 1481 2.86 - 4.30: 243 4.30 - 5.73: 43 5.73 - 7.16: 16 Bond angle restraints: 13685 Sorted by residual: angle pdb=" O4' DC J 119 " pdb=" C1' DC J 119 " pdb=" N1 DC J 119 " ideal model delta sigma weight residual 108.00 113.05 -5.05 7.00e-01 2.04e+00 5.20e+01 angle pdb=" O5' DA I 117 " pdb=" C5' DA I 117 " pdb=" C4' DA I 117 " ideal model delta sigma weight residual 109.40 115.11 -5.71 8.00e-01 1.56e+00 5.09e+01 angle pdb=" O4' DG I 41 " pdb=" C1' DG I 41 " pdb=" N9 DG I 41 " ideal model delta sigma weight residual 108.00 103.61 4.39 7.00e-01 2.04e+00 3.93e+01 angle pdb=" O4' DG I 38 " pdb=" C1' DG I 38 " pdb=" N9 DG I 38 " ideal model delta sigma weight residual 108.00 103.78 4.22 7.00e-01 2.04e+00 3.64e+01 angle pdb=" O5' DG I 39 " pdb=" C5' DG I 39 " pdb=" C4' DG I 39 " ideal model delta sigma weight residual 109.40 114.12 -4.72 8.00e-01 1.56e+00 3.48e+01 ... (remaining 13680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 4355 33.38 - 66.75: 879 66.75 - 100.13: 17 100.13 - 133.51: 1 133.51 - 166.88: 6 Dihedral angle restraints: 5258 sinusoidal: 3340 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual 220.00 53.12 166.88 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 65.43 154.57 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS C 92 " pdb=" C HIS C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1437 0.103 - 0.206: 142 0.206 - 0.309: 5 0.309 - 0.412: 0 0.412 - 0.515: 2 Chirality restraints: 1586 Sorted by residual: chirality pdb=" C1' DG I 53 " pdb=" O4' DG I 53 " pdb=" C2' DG I 53 " pdb=" N9 DG I 53 " both_signs ideal model delta sigma weight residual False 2.43 1.92 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" C1' DT I 57 " pdb=" O4' DT I 57 " pdb=" C2' DT I 57 " pdb=" N1 DT I 57 " both_signs ideal model delta sigma weight residual False 2.43 1.99 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C1' DC J 28 " pdb=" O4' DC J 28 " pdb=" C2' DC J 28 " pdb=" N1 DC J 28 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1583 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 117 " 0.021 2.00e-02 2.50e+03 4.80e-02 6.33e+01 pdb=" N9 DA I 117 " -0.122 2.00e-02 2.50e+03 pdb=" C8 DA I 117 " 0.095 2.00e-02 2.50e+03 pdb=" N7 DA I 117 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DA I 117 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 117 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 117 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 117 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 117 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DA I 117 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA I 117 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 116 " 0.038 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" N1 DC J 116 " -0.095 2.00e-02 2.50e+03 pdb=" C2 DC J 116 " 0.057 2.00e-02 2.50e+03 pdb=" O2 DC J 116 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC J 116 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 116 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 116 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 116 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DC J 116 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 32 " -0.063 2.00e-02 2.50e+03 2.80e-02 2.36e+01 pdb=" N9 DG I 32 " 0.070 2.00e-02 2.50e+03 pdb=" C8 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 32 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG I 32 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 32 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 32 " 0.006 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 831 2.72 - 3.26: 7789 3.26 - 3.81: 16217 3.81 - 4.35: 21301 4.35 - 4.90: 30325 Nonbonded interactions: 76463 Sorted by model distance: nonbonded pdb=" OE1 GLU D 76 " pdb=" NH2 ARG D 79 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLU H 76 " pdb=" NH2 ARG H 79 " model vdw 2.170 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.248 3.120 nonbonded pdb=" N2 DG I 32 " pdb=" O2 DC J 116 " model vdw 2.254 3.120 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 2.267 3.120 ... (remaining 76458 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' } ncs_group { reference = chain 'D' 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: 0.930 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.055 9539 Z= 0.661 Angle : 1.016 7.159 13685 Z= 0.820 Chirality : 0.064 0.515 1586 Planarity : 0.010 0.062 1080 Dihedral : 25.701 166.884 4014 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.14 % Allowed : 2.85 % Favored : 95.02 % 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: -6.14 (0.18), residues: 640 helix: -4.12 (0.10), residues: 458 sheet: None (None), residues: 0 loop : -3.19 (0.32), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.026 0.003 TYR B 51 PHE 0.021 0.002 PHE A 67 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.66 ( 9539) covalent geometry : angle 1.01567 / 0.82 (13685) hydrogen bonds : bond 0.14542 / 15.71 ( 494) hydrogen bonds : angle 6.10090 / 7.89 ( 1307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.241 Fit side-chains REVERT: B 84 MET cc_start: 0.7144 (mmm) cc_final: 0.6922 (tpp) REVERT: C 89 MET cc_start: 0.7912 (ptt) cc_final: 0.7111 (tpt) REVERT: G 89 MET cc_start: 0.7988 (ptt) cc_final: 0.7159 (tpt) outliers start: 12 outliers final: 0 residues processed: 168 average time/residue: 0.5573 time to fit residues: 99.6156 Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 84 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 84 ASN H 109 HIS C 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.188134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163983 restraints weight = 11376.217| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.08 r_work: 0.3755 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9539 Z= 0.168 Angle : 0.709 8.376 13685 Z= 0.414 Chirality : 0.048 0.333 1586 Planarity : 0.006 0.060 1080 Dihedral : 30.553 172.359 2754 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.96 % Allowed : 14.41 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.28), residues: 640 helix: -1.42 (0.20), residues: 478 sheet: None (None), residues: 0 loop : -2.35 (0.39), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.017 0.002 TYR F 51 PHE 0.011 0.002 PHE A 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 ( 9539) covalent geometry : angle 0.70866 / 0.41 (13685) hydrogen bonds : bond 0.05536 / 6.04 ( 494) hydrogen bonds : angle 3.73369 / 4.95 ( 1307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.216 Fit side-chains REVERT: A 71 VAL cc_start: 0.9053 (t) cc_final: 0.8837 (t) REVERT: A 73 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: B 84 MET cc_start: 0.7958 (mmm) cc_final: 0.7698 (tpp) REVERT: E 73 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: E 129 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7695 (ttt-90) REVERT: E 131 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8595 (mtp85) REVERT: C 89 MET cc_start: 0.8231 (ptt) cc_final: 0.7620 (tpt) REVERT: G 89 MET cc_start: 0.8291 (ptt) cc_final: 0.7630 (tpt) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.5203 time to fit residues: 75.6450 Evaluate side-chains 136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 109 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153919 restraints weight = 11245.252| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.06 r_work: 0.3642 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9539 Z= 0.195 Angle : 0.714 9.557 13685 Z= 0.404 Chirality : 0.050 0.364 1586 Planarity : 0.006 0.047 1080 Dihedral : 31.240 175.688 2754 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.56 % Allowed : 13.70 % Favored : 82.74 % 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: -0.68 (0.31), residues: 640 helix: 0.04 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.72 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.021 0.002 TYR F 51 PHE 0.019 0.003 PHE G 29 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 ( 9539) covalent geometry : angle 0.71444 / 0.40 (13685) hydrogen bonds : bond 0.05381 / 5.74 ( 494) hydrogen bonds : angle 3.41554 / 4.46 ( 1307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.193 Fit side-chains REVERT: A 73 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6759 (tp30) REVERT: B 84 MET cc_start: 0.8141 (mmm) cc_final: 0.7875 (tpp) REVERT: E 73 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: C 49 ARG cc_start: 0.7729 (tpt170) cc_final: 0.7459 (ttm170) REVERT: G 49 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7454 (ttm170) outliers start: 20 outliers final: 10 residues processed: 132 average time/residue: 0.5316 time to fit residues: 74.6373 Evaluate side-chains 136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151767 restraints weight = 11252.040| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.03 r_work: 0.3625 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9539 Z= 0.173 Angle : 0.661 9.172 13685 Z= 0.377 Chirality : 0.047 0.374 1586 Planarity : 0.005 0.045 1080 Dihedral : 31.272 179.666 2754 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.38 % Allowed : 17.79 % Favored : 78.83 % 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: 0.21 (0.32), residues: 640 helix: 0.74 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 39 TYR 0.013 0.001 TYR F 51 PHE 0.016 0.002 PHE C 29 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 9539) covalent geometry : angle 0.66141 / 0.38 (13685) hydrogen bonds : bond 0.04741 / 5.08 ( 494) hydrogen bonds : angle 3.22808 / 4.24 ( 1307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: B 84 MET cc_start: 0.8147 (mmm) cc_final: 0.7922 (tpp) REVERT: D 38 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8744 (m) REVERT: E 73 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6702 (tp30) REVERT: H 42 TYR cc_start: 0.7724 (t80) cc_final: 0.6960 (t80) REVERT: G 49 ARG cc_start: 0.7654 (tpt170) cc_final: 0.7406 (ttm170) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.6012 time to fit residues: 83.3834 Evaluate side-chains 137 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 overall best weight: 0.6096 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.177692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153670 restraints weight = 11239.715| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.03 r_work: 0.3642 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9539 Z= 0.135 Angle : 0.630 9.242 13685 Z= 0.362 Chirality : 0.045 0.369 1586 Planarity : 0.005 0.041 1080 Dihedral : 31.311 179.641 2754 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.38 % Allowed : 19.57 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.32), residues: 640 helix: 1.09 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.011 0.001 TYR B 51 PHE 0.012 0.001 PHE C 29 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 ( 9539) covalent geometry : angle 0.62983 / 0.36 (13685) hydrogen bonds : bond 0.04459 / 4.81 ( 494) hydrogen bonds : angle 3.13431 / 4.14 ( 1307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.7953 (mtt-85) REVERT: A 73 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: B 84 MET cc_start: 0.8176 (mmm) cc_final: 0.7969 (tpp) REVERT: D 38 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8764 (m) REVERT: E 72 ARG cc_start: 0.8469 (mtt-85) cc_final: 0.8254 (mtt-85) REVERT: H 42 TYR cc_start: 0.7726 (t80) cc_final: 0.6961 (t80) REVERT: G 49 ARG cc_start: 0.7599 (tpt170) cc_final: 0.7394 (ttm170) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.5837 time to fit residues: 80.7785 Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 0.0770 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154696 restraints weight = 11311.075| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.04 r_work: 0.3663 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9539 Z= 0.129 Angle : 0.608 8.982 13685 Z= 0.351 Chirality : 0.044 0.372 1586 Planarity : 0.005 0.043 1080 Dihedral : 31.318 176.654 2754 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.38 % Allowed : 19.22 % Favored : 77.40 % 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: 1.09 (0.32), residues: 640 helix: 1.42 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.45 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.011 0.001 TYR G 61 PHE 0.006 0.001 PHE C 29 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 ( 9539) covalent geometry : angle 0.60799 / 0.35 (13685) hydrogen bonds : bond 0.04314 / 4.65 ( 494) hydrogen bonds : angle 3.02476 / 3.97 ( 1307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.7970 (mtt-85) REVERT: B 84 MET cc_start: 0.8191 (mmm) cc_final: 0.7989 (tpp) REVERT: D 38 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8801 (m) REVERT: H 42 TYR cc_start: 0.7656 (t80) cc_final: 0.6950 (t80) REVERT: C 24 ARG cc_start: 0.5719 (ttt-90) cc_final: 0.5482 (ttt-90) REVERT: G 49 ARG cc_start: 0.7622 (tpt170) cc_final: 0.7363 (ttm170) outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 0.5769 time to fit residues: 83.2327 Evaluate side-chains 135 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.179013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154374 restraints weight = 11301.632| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.04 r_work: 0.3666 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9539 Z= 0.131 Angle : 0.607 8.694 13685 Z= 0.348 Chirality : 0.043 0.377 1586 Planarity : 0.004 0.041 1080 Dihedral : 31.242 171.761 2754 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.49 % Allowed : 20.82 % Favored : 76.69 % 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: 1.36 (0.32), residues: 640 helix: 1.65 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.012 0.001 TYR C 61 PHE 0.006 0.001 PHE A 78 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 ( 9539) covalent geometry : angle 0.60703 / 0.35 (13685) hydrogen bonds : bond 0.04188 / 4.51 ( 494) hydrogen bonds : angle 2.96257 / 3.94 ( 1307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.223 Fit side-chains REVERT: A 72 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8006 (mtt-85) REVERT: D 86 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7034 (mtt90) REVERT: E 72 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8293 (mtt-85) REVERT: H 42 TYR cc_start: 0.7568 (t80) cc_final: 0.6923 (t80) REVERT: G 47 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8248 (mp) REVERT: G 49 ARG cc_start: 0.7624 (tpt170) cc_final: 0.7356 (ttm170) outliers start: 14 outliers final: 9 residues processed: 128 average time/residue: 0.5782 time to fit residues: 78.2826 Evaluate side-chains 131 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.174040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149486 restraints weight = 11101.116| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.04 r_work: 0.3602 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9539 Z= 0.167 Angle : 0.636 8.722 13685 Z= 0.360 Chirality : 0.045 0.380 1586 Planarity : 0.005 0.042 1080 Dihedral : 31.282 175.430 2754 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.56 % Allowed : 20.64 % Favored : 75.80 % 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: 1.37 (0.32), residues: 640 helix: 1.65 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.013 0.001 TYR F 51 PHE 0.011 0.002 PHE C 29 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 9539) covalent geometry : angle 0.63553 / 0.36 (13685) hydrogen bonds : bond 0.04443 / 4.74 ( 494) hydrogen bonds : angle 3.04112 / 4.04 ( 1307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.8247 (mtt-85) REVERT: H 42 TYR cc_start: 0.7612 (t80) cc_final: 0.6920 (t80) REVERT: G 47 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8194 (mp) REVERT: G 49 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7425 (ttm170) outliers start: 20 outliers final: 10 residues processed: 137 average time/residue: 0.5593 time to fit residues: 81.3252 Evaluate side-chains 139 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.174328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149745 restraints weight = 11129.100| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.04 r_work: 0.3612 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9539 Z= 0.141 Angle : 0.638 8.588 13685 Z= 0.358 Chirality : 0.045 0.378 1586 Planarity : 0.005 0.041 1080 Dihedral : 31.288 174.643 2754 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.67 % Allowed : 21.71 % Favored : 75.62 % 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: 1.41 (0.32), residues: 640 helix: 1.67 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.48 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.012 0.001 TYR C 61 PHE 0.015 0.001 PHE C 29 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 9539) covalent geometry : angle 0.63760 / 0.36 (13685) hydrogen bonds : bond 0.04292 / 4.57 ( 494) hydrogen bonds : angle 3.04423 / 4.05 ( 1307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8469 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: A 73 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: H 42 TYR cc_start: 0.7595 (t80) cc_final: 0.6910 (t80) REVERT: G 47 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8176 (mp) REVERT: G 49 ARG cc_start: 0.7659 (tpt170) cc_final: 0.7400 (ttm170) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 0.5730 time to fit residues: 81.3982 Evaluate side-chains 140 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.174736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150135 restraints weight = 11164.900| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.04 r_work: 0.3616 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9539 Z= 0.135 Angle : 0.629 8.625 13685 Z= 0.355 Chirality : 0.044 0.378 1586 Planarity : 0.005 0.041 1080 Dihedral : 31.291 174.300 2754 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 22.60 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.32), residues: 640 helix: 1.70 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.013 0.001 TYR C 61 PHE 0.010 0.001 PHE C 29 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 9539) covalent geometry : angle 0.62934 / 0.36 (13685) hydrogen bonds : bond 0.04241 / 4.53 ( 494) hydrogen bonds : angle 3.03029 / 4.02 ( 1307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8235 (mtt-85) REVERT: A 73 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6717 (tp30) REVERT: H 42 TYR cc_start: 0.7607 (t80) cc_final: 0.6917 (t80) REVERT: G 49 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7410 (ttm170) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.5676 time to fit residues: 78.7038 Evaluate side-chains 139 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.174959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150464 restraints weight = 11054.076| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.04 r_work: 0.3618 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9539 Z= 0.140 Angle : 0.630 8.604 13685 Z= 0.355 Chirality : 0.044 0.377 1586 Planarity : 0.005 0.042 1080 Dihedral : 31.291 174.046 2754 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 22.60 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.32), residues: 640 helix: 1.70 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.012 0.001 TYR C 61 PHE 0.011 0.001 PHE C 29 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 ( 9539) covalent geometry : angle 0.62999 / 0.35 (13685) hydrogen bonds : bond 0.04203 / 4.49 ( 494) hydrogen bonds : angle 3.02080 / 4.01 ( 1307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.11 seconds wall clock time: 45 minutes 25.58 seconds (2725.58 seconds total)