Starting phenix.real_space_refine on Sat Sep 12 00:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.map" model { file = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7by0_30239/09_2026/7by0_30239.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 12 5.16 5 C 7083 2.51 5 N 2407 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 12693 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2914 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2949 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 363 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 366 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 2.77, per 1000 atoms: 0.22 Number of scatterers: 12693 At special positions: 0 Unit cell: (86.9, 123.2, 115.5, 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 12 16.00 P 288 15.00 O 2903 8.00 N 2407 7.00 C 7083 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: 0.93 Conformation dependent library (CDL) restraints added in 340.2 milliseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 65.6% alpha, 1.2% beta 140 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.595A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.582A pdb=" N ALA A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.766A pdb=" N LEU A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.042A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.828A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.624A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.491A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.827A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.611A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.870A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.543A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 removed outlier: 3.558A pdb=" N LEU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 133 removed outlier: 3.641A pdb=" N LEU E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 138 removed outlier: 4.000A pdb=" N GLN E 137 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 138' Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.680A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.953A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.402A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.955A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.606A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.724A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 629 through 640 removed outlier: 3.964A pdb=" N LYS K 633 " --> pdb=" O HIS K 629 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 636 " --> pdb=" O ILE K 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 629 through 640 removed outlier: 4.107A pdb=" N LYS L 633 " --> pdb=" O HIS L 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.069A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.150A pdb=" N ARG E 86 " --> 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 'G' and resid 42 through 43 removed outlier: 7.433A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 385 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.27 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: 2364 1.33 - 1.45: 4427 1.45 - 1.57: 6115 1.57 - 1.69: 576 1.69 - 1.81: 20 Bond restraints: 13502 Sorted by residual: bond pdb=" C1' DA J 165 " pdb=" N9 DA J 165 " ideal model delta sigma weight residual 1.468 1.370 0.098 1.40e-02 5.10e+03 4.92e+01 bond pdb=" OG1 TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" N9 DA I 60 " pdb=" C4 DA I 60 " ideal model delta sigma weight residual 1.374 1.342 0.032 6.00e-03 2.78e+04 2.76e+01 bond pdb=" C1' DC I 52 " pdb=" N1 DC I 52 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.56e+01 ... (remaining 13497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18583 2.36 - 4.73: 829 4.73 - 7.09: 49 7.09 - 9.45: 10 9.45 - 11.81: 2 Bond angle restraints: 19473 Sorted by residual: angle pdb=" O4' DG I 32 " pdb=" C4' DG I 32 " pdb=" C3' DG I 32 " ideal model delta sigma weight residual 106.00 101.60 4.40 6.00e-01 2.78e+00 5.39e+01 angle pdb=" O4' DC I 55 " pdb=" C4' DC I 55 " pdb=" C3' DC I 55 " ideal model delta sigma weight residual 106.00 102.10 3.90 6.00e-01 2.78e+00 4.23e+01 angle pdb=" O4' DC J 286 " pdb=" C4' DC J 286 " pdb=" C3' DC J 286 " ideal model delta sigma weight residual 106.00 102.20 3.80 6.00e-01 2.78e+00 4.02e+01 angle pdb=" O4' DA J 163 " pdb=" C4' DA J 163 " pdb=" C3' DA J 163 " ideal model delta sigma weight residual 106.00 102.25 3.75 6.00e-01 2.78e+00 3.91e+01 angle pdb=" O4' DG J 226 " pdb=" C4' DG J 226 " pdb=" C3' DG J 226 " ideal model delta sigma weight residual 106.00 102.34 3.66 6.00e-01 2.78e+00 3.72e+01 ... (remaining 19468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 4790 22.35 - 44.69: 1469 44.69 - 67.04: 1002 67.04 - 89.39: 115 89.39 - 111.74: 8 Dihedral angle restraints: 7384 sinusoidal: 4864 harmonic: 2520 Sorted by residual: dihedral pdb=" CA ARG E 41 " pdb=" C ARG E 41 " pdb=" N TYR E 42 " pdb=" CA TYR E 42 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU K 662 " pdb=" C LEU K 662 " pdb=" N LYS K 663 " pdb=" CA LYS K 663 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1684 0.058 - 0.115: 436 0.115 - 0.173: 83 0.173 - 0.231: 9 0.231 - 0.289: 1 Chirality restraints: 2213 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE L 660 " pdb=" CA ILE L 660 " pdb=" CG1 ILE L 660 " pdb=" CG2 ILE L 660 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2210 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 120 " 0.035 2.00e-02 2.50e+03 1.55e-02 7.24e+00 pdb=" N9 DG I 120 " -0.035 2.00e-02 2.50e+03 pdb=" C8 DG I 120 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 120 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DG I 120 " 0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 120 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 120 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 120 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 120 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 18 " -0.036 2.00e-02 2.50e+03 1.54e-02 7.14e+00 pdb=" N9 DG I 18 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 18 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 18 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 18 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG I 18 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 18 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 18 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 18 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG I 18 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 18 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 665 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C LEU K 665 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU K 665 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU K 666 " -0.015 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 140 2.54 - 3.13: 9094 3.13 - 3.72: 26032 3.72 - 4.31: 32371 4.31 - 4.90: 45647 Nonbonded interactions: 113284 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 659 " model vdw 1.950 3.120 nonbonded pdb=" OE2 GLU G 92 " pdb=" NH1 ARG L 659 " model vdw 2.048 3.120 nonbonded pdb=" OE1 GLU D 105 " pdb=" N ILE K 660 " model vdw 2.206 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR E 80 " pdb=" O VAL E 83 " model vdw 2.254 3.040 ... (remaining 113279 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 11 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 31 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 124)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 628 through 644 or (resid 645 and (name N or name CA or na \ me C or name O or name CB )) or resid 646 through 679)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 0.111 13502 Z= 0.721 Angle : 1.068 11.815 19473 Z= 0.888 Chirality : 0.054 0.289 2213 Planarity : 0.007 0.060 1473 Dihedral : 31.228 111.735 5756 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.47 % 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: -3.59 (0.22), residues: 838 helix: -2.11 (0.16), residues: 532 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.014 0.002 TYR F 98 PHE 0.015 0.003 PHE E 79 TRP 0.015 0.003 TRP L 668 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.72 (13502) covalent geometry : angle 1.06778 / 0.89 (19473) hydrogen bonds : bond 0.13530 / 8.87 ( 745) hydrogen bonds : angle 5.31064 / 3.63 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9464 (m-10) cc_final: 0.9135 (m-10) REVERT: A 74 GLU cc_start: 0.8962 (tt0) cc_final: 0.8329 (mt-10) REVERT: A 85 TYR cc_start: 0.9499 (m-80) cc_final: 0.9244 (m-80) REVERT: A 128 GLN cc_start: 0.9521 (mt0) cc_final: 0.9295 (mm-40) REVERT: A 131 ARG cc_start: 0.9357 (ttt-90) cc_final: 0.9132 (ptm160) REVERT: B 60 VAL cc_start: 0.9565 (m) cc_final: 0.9062 (p) REVERT: B 62 LEU cc_start: 0.9796 (mm) cc_final: 0.9568 (pp) REVERT: B 63 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9029 (pt0) REVERT: B 74 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9217 (tm-30) REVERT: B 84 MET cc_start: 0.9404 (mmm) cc_final: 0.8993 (mmm) REVERT: C 36 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9018 (mmtp) REVERT: C 61 GLU cc_start: 0.9089 (tp30) cc_final: 0.8830 (mm-30) REVERT: C 75 LYS cc_start: 0.9786 (mmtt) cc_final: 0.9492 (mmtm) REVERT: C 87 ILE cc_start: 0.9864 (mm) cc_final: 0.9465 (tp) REVERT: C 95 LYS cc_start: 0.9820 (ttmt) cc_final: 0.9505 (tptp) REVERT: D 80 LEU cc_start: 0.9736 (tp) cc_final: 0.9531 (tt) REVERT: D 99 ARG cc_start: 0.9422 (mtt180) cc_final: 0.8805 (ttm110) REVERT: E 55 TYR cc_start: 0.9609 (m-10) cc_final: 0.9364 (m-10) REVERT: E 85 TYR cc_start: 0.9350 (m-10) cc_final: 0.9134 (m-80) REVERT: E 90 MET cc_start: 0.9315 (tmm) cc_final: 0.9022 (ppp) REVERT: E 95 LEU cc_start: 0.9883 (tp) cc_final: 0.9667 (pp) REVERT: E 100 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9294 (mt-10) REVERT: E 128 GLN cc_start: 0.9605 (tt0) cc_final: 0.8823 (tp-100) REVERT: F 31 LYS cc_start: 0.9743 (pptt) cc_final: 0.9510 (ptmm) REVERT: F 59 LYS cc_start: 0.9669 (ttpp) cc_final: 0.9426 (ptmm) REVERT: F 60 VAL cc_start: 0.9472 (m) cc_final: 0.8984 (p) REVERT: F 62 LEU cc_start: 0.9842 (mm) cc_final: 0.9579 (pp) REVERT: F 63 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9033 (mt-10) REVERT: F 74 GLU cc_start: 0.9548 (tt0) cc_final: 0.9147 (tm-30) REVERT: F 79 LYS cc_start: 0.9670 (mmtm) cc_final: 0.8925 (ttpp) REVERT: G 78 ILE cc_start: 0.9717 (mt) cc_final: 0.9330 (tp) REVERT: G 95 LYS cc_start: 0.9794 (tttm) cc_final: 0.9579 (tptm) REVERT: H 68 ASP cc_start: 0.9233 (t70) cc_final: 0.8948 (t0) REVERT: H 71 GLU cc_start: 0.9234 (pp20) cc_final: 0.9027 (pp20) REVERT: H 72 ARG cc_start: 0.9554 (ttm170) cc_final: 0.9329 (ptp-110) REVERT: H 80 LEU cc_start: 0.9463 (tp) cc_final: 0.9090 (tp) REVERT: H 99 ARG cc_start: 0.9499 (mtt90) cc_final: 0.8716 (ttm110) REVERT: L 665 LEU cc_start: 0.9255 (tt) cc_final: 0.9041 (tp) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.1313 time to fit residues: 37.4675 Evaluate side-chains 142 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 96 GLN B 25 ASN B 27 GLN C 38 ASN C 104 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN E 128 GLN F 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 49 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.023000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.019176 restraints weight = 171515.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.019959 restraints weight = 86644.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.020489 restraints weight = 53258.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.020872 restraints weight = 36448.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.021144 restraints weight = 26913.602| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13502 Z= 0.190 Angle : 0.806 9.187 19473 Z= 0.465 Chirality : 0.058 0.276 2213 Planarity : 0.006 0.051 1473 Dihedral : 35.087 121.045 4104 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.77 % 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: -1.82 (0.26), residues: 838 helix: -0.54 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -2.37 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 79 TYR 0.023 0.002 TYR F 72 PHE 0.013 0.002 PHE E 68 TRP 0.007 0.002 TRP K 668 HIS 0.007 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.19 (13502) covalent geometry : angle 0.80632 / 0.47 (19473) hydrogen bonds : bond 0.07690 / 5.13 ( 745) hydrogen bonds : angle 4.29463 / 2.95 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9491 (m-10) cc_final: 0.9059 (m-10) REVERT: A 74 GLU cc_start: 0.9057 (tt0) cc_final: 0.8418 (mt-10) REVERT: A 85 TYR cc_start: 0.9540 (m-80) cc_final: 0.9103 (m-80) REVERT: A 131 ARG cc_start: 0.9465 (ttt-90) cc_final: 0.9070 (ptm160) REVERT: B 54 THR cc_start: 0.9820 (p) cc_final: 0.9548 (p) REVERT: B 59 LYS cc_start: 0.9696 (ptmt) cc_final: 0.9462 (ptmm) REVERT: B 62 LEU cc_start: 0.9785 (mm) cc_final: 0.9566 (pp) REVERT: B 63 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8986 (mt-10) REVERT: B 74 GLU cc_start: 0.9499 (tm-30) cc_final: 0.9221 (tm-30) REVERT: B 84 MET cc_start: 0.9411 (mmm) cc_final: 0.9051 (mmm) REVERT: C 36 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9036 (mmtp) REVERT: C 75 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9427 (mmtm) REVERT: C 87 ILE cc_start: 0.9747 (mm) cc_final: 0.9400 (tp) REVERT: C 91 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9039 (pp20) REVERT: C 95 LYS cc_start: 0.9842 (ttmt) cc_final: 0.9633 (tptm) REVERT: D 72 ARG cc_start: 0.9600 (ttm170) cc_final: 0.9196 (ptm160) REVERT: D 99 ARG cc_start: 0.9385 (mtt180) cc_final: 0.8756 (ttm110) REVERT: D 113 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9327 (mt-10) REVERT: E 68 PHE cc_start: 0.9546 (t80) cc_final: 0.9119 (t80) REVERT: E 96 GLN cc_start: 0.9190 (tp40) cc_final: 0.8674 (tp40) REVERT: E 97 GLU cc_start: 0.9381 (tt0) cc_final: 0.8680 (tt0) REVERT: E 100 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9045 (mt-10) REVERT: E 128 GLN cc_start: 0.9684 (OUTLIER) cc_final: 0.9287 (mm-40) REVERT: F 49 LEU cc_start: 0.9518 (mp) cc_final: 0.9195 (mp) REVERT: F 60 VAL cc_start: 0.9544 (m) cc_final: 0.9100 (p) REVERT: F 63 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9069 (mt-10) REVERT: F 74 GLU cc_start: 0.9575 (tt0) cc_final: 0.9163 (tm-30) REVERT: F 79 LYS cc_start: 0.9654 (mptt) cc_final: 0.9193 (ttpp) REVERT: F 84 MET cc_start: 0.9652 (mmp) cc_final: 0.9450 (mmm) REVERT: G 78 ILE cc_start: 0.9718 (mt) cc_final: 0.9299 (tp) REVERT: G 87 ILE cc_start: 0.9811 (mm) cc_final: 0.9537 (tp) REVERT: H 59 MET cc_start: 0.8903 (tpt) cc_final: 0.8597 (tpp) REVERT: H 72 ARG cc_start: 0.9611 (ttm170) cc_final: 0.9409 (ptm160) REVERT: H 80 LEU cc_start: 0.9643 (tp) cc_final: 0.9259 (tp) REVERT: H 99 ARG cc_start: 0.9500 (mtt90) cc_final: 0.8775 (ttm110) REVERT: K 662 LEU cc_start: 0.9413 (mm) cc_final: 0.9097 (mm) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1167 time to fit residues: 31.1529 Evaluate side-chains 142 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 78 optimal weight: 50.0000 chunk 74 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.022390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.018675 restraints weight = 183674.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.019414 restraints weight = 93113.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.019930 restraints weight = 57350.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.020289 restraints weight = 39298.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.020554 restraints weight = 29174.395| |-----------------------------------------------------------------------------| r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13502 Z= 0.239 Angle : 0.812 8.466 19473 Z= 0.466 Chirality : 0.057 0.257 2213 Planarity : 0.006 0.054 1473 Dihedral : 35.052 126.140 4104 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -1.12 (0.27), residues: 838 helix: 0.12 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.39 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.025 0.002 TYR F 51 PHE 0.011 0.002 PHE A 68 TRP 0.008 0.002 TRP E 87 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.24 (13502) covalent geometry : angle 0.81247 / 0.47 (19473) hydrogen bonds : bond 0.09136 / 6.15 ( 745) hydrogen bonds : angle 4.27643 / 2.94 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9647 (mp0) cc_final: 0.9350 (mp0) REVERT: A 55 TYR cc_start: 0.9502 (m-10) cc_final: 0.9058 (m-10) REVERT: A 74 GLU cc_start: 0.9072 (tt0) cc_final: 0.8486 (mt-10) REVERT: A 85 TYR cc_start: 0.9514 (m-80) cc_final: 0.9110 (m-80) REVERT: A 131 ARG cc_start: 0.9528 (ttt-90) cc_final: 0.8930 (ptm-80) REVERT: B 59 LYS cc_start: 0.9690 (ptmt) cc_final: 0.9317 (ptmm) REVERT: B 62 LEU cc_start: 0.9793 (mm) cc_final: 0.9511 (pp) REVERT: B 63 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8922 (mp0) REVERT: B 84 MET cc_start: 0.9440 (mmm) cc_final: 0.9214 (mmt) REVERT: C 36 LYS cc_start: 0.9503 (mtpt) cc_final: 0.9092 (mmtp) REVERT: C 87 ILE cc_start: 0.9772 (mm) cc_final: 0.9458 (tp) REVERT: C 95 LYS cc_start: 0.9847 (ttmt) cc_final: 0.9645 (tptp) REVERT: D 72 ARG cc_start: 0.9604 (ttm170) cc_final: 0.9374 (ptm160) REVERT: D 99 ARG cc_start: 0.9414 (mtt180) cc_final: 0.8794 (ttm110) REVERT: E 55 TYR cc_start: 0.9680 (m-10) cc_final: 0.9479 (m-10) REVERT: E 68 PHE cc_start: 0.9535 (t80) cc_final: 0.9122 (t80) REVERT: E 90 MET cc_start: 0.9156 (tmm) cc_final: 0.8888 (tmm) REVERT: E 96 GLN cc_start: 0.9222 (tp40) cc_final: 0.8886 (tp40) REVERT: E 97 GLU cc_start: 0.9378 (tt0) cc_final: 0.8662 (tt0) REVERT: E 100 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9114 (mt-10) REVERT: E 128 GLN cc_start: 0.9747 (tt0) cc_final: 0.9391 (tp-100) REVERT: F 59 LYS cc_start: 0.9702 (ptmm) cc_final: 0.9459 (ptmm) REVERT: F 60 VAL cc_start: 0.9629 (m) cc_final: 0.9135 (p) REVERT: F 63 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8967 (mt-10) REVERT: F 74 GLU cc_start: 0.9602 (tt0) cc_final: 0.9166 (tm-30) REVERT: F 79 LYS cc_start: 0.9667 (mptt) cc_final: 0.9198 (ttpp) REVERT: G 73 ASN cc_start: 0.9446 (t0) cc_final: 0.9168 (m110) REVERT: G 78 ILE cc_start: 0.9761 (mt) cc_final: 0.9350 (tp) REVERT: G 87 ILE cc_start: 0.9825 (mm) cc_final: 0.9528 (tp) REVERT: G 91 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8856 (mm-30) REVERT: G 95 LYS cc_start: 0.9677 (tttp) cc_final: 0.9416 (tptm) REVERT: H 59 MET cc_start: 0.8938 (tpt) cc_final: 0.8651 (tpp) REVERT: H 72 ARG cc_start: 0.9688 (ttm170) cc_final: 0.9436 (ptm160) REVERT: H 80 LEU cc_start: 0.9686 (tp) cc_final: 0.9345 (tp) REVERT: H 99 ARG cc_start: 0.9544 (mtt90) cc_final: 0.8818 (ttm110) REVERT: H 113 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8443 (tm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1319 time to fit residues: 32.9396 Evaluate side-chains 136 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 40.0000 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 96 GLN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.022895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.019152 restraints weight = 173819.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.019923 restraints weight = 85175.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.020460 restraints weight = 51299.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.020831 restraints weight = 34641.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.021092 restraints weight = 25379.524| |-----------------------------------------------------------------------------| r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13502 Z= 0.173 Angle : 0.743 10.506 19473 Z= 0.428 Chirality : 0.054 0.245 2213 Planarity : 0.005 0.050 1473 Dihedral : 35.062 129.948 4104 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -0.63 (0.28), residues: 838 helix: 0.54 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.27 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 669 TYR 0.022 0.002 TYR F 51 PHE 0.012 0.002 PHE A 68 TRP 0.006 0.002 TRP L 668 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (13502) covalent geometry : angle 0.74253 / 0.43 (19473) hydrogen bonds : bond 0.07157 / 4.82 ( 745) hydrogen bonds : angle 4.03331 / 2.78 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9489 (m-10) cc_final: 0.9042 (m-10) REVERT: A 66 GLN cc_start: 0.9720 (mm-40) cc_final: 0.9334 (mp10) REVERT: A 74 GLU cc_start: 0.9021 (tt0) cc_final: 0.8383 (mt-10) REVERT: A 85 TYR cc_start: 0.9516 (m-80) cc_final: 0.9094 (m-80) REVERT: A 97 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9021 (mt-10) REVERT: A 100 GLU cc_start: 0.9532 (mt-10) cc_final: 0.9050 (mt-10) REVERT: B 59 LYS cc_start: 0.9682 (ptmt) cc_final: 0.9404 (ptmm) REVERT: B 62 LEU cc_start: 0.9789 (mm) cc_final: 0.9573 (pp) REVERT: B 63 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8885 (mt-10) REVERT: C 36 LYS cc_start: 0.9508 (mtpt) cc_final: 0.9049 (mmtp) REVERT: C 87 ILE cc_start: 0.9755 (mm) cc_final: 0.9422 (tp) REVERT: D 72 ARG cc_start: 0.9599 (ttm170) cc_final: 0.9395 (ptm160) REVERT: D 99 ARG cc_start: 0.9389 (mtt180) cc_final: 0.8778 (ttm110) REVERT: E 68 PHE cc_start: 0.9536 (t80) cc_final: 0.9062 (t80) REVERT: E 74 GLU cc_start: 0.9526 (tt0) cc_final: 0.9315 (pt0) REVERT: E 90 MET cc_start: 0.9172 (tmm) cc_final: 0.8877 (tmm) REVERT: E 96 GLN cc_start: 0.9266 (tp-100) cc_final: 0.8667 (tp40) REVERT: E 97 GLU cc_start: 0.9396 (tt0) cc_final: 0.8704 (tt0) REVERT: E 100 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9128 (mt-10) REVERT: E 128 GLN cc_start: 0.9696 (tt0) cc_final: 0.8980 (tp-100) REVERT: F 59 LYS cc_start: 0.9698 (ptmm) cc_final: 0.9388 (ptmm) REVERT: F 60 VAL cc_start: 0.9560 (m) cc_final: 0.9095 (p) REVERT: F 63 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8986 (mp0) REVERT: F 74 GLU cc_start: 0.9570 (tt0) cc_final: 0.9131 (tm-30) REVERT: F 79 LYS cc_start: 0.9656 (mptt) cc_final: 0.9183 (ttpp) REVERT: G 36 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8851 (mmmt) REVERT: G 73 ASN cc_start: 0.9246 (t0) cc_final: 0.8980 (m110) REVERT: G 78 ILE cc_start: 0.9765 (mt) cc_final: 0.9343 (tp) REVERT: G 91 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8353 (mm-30) REVERT: G 92 GLU cc_start: 0.8996 (pm20) cc_final: 0.8703 (mt-10) REVERT: G 95 LYS cc_start: 0.9675 (tttp) cc_final: 0.9443 (tptt) REVERT: H 72 ARG cc_start: 0.9669 (ttm170) cc_final: 0.9447 (ptm160) REVERT: H 80 LEU cc_start: 0.9650 (tp) cc_final: 0.9334 (tp) REVERT: H 99 ARG cc_start: 0.9526 (mtt90) cc_final: 0.8786 (ttm110) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1277 time to fit residues: 33.1805 Evaluate side-chains 136 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 66 GLN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.022948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.019171 restraints weight = 173501.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.019945 restraints weight = 85299.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.020477 restraints weight = 51583.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.020842 restraints weight = 34907.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.021107 restraints weight = 25672.061| |-----------------------------------------------------------------------------| r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13502 Z= 0.176 Angle : 0.732 8.644 19473 Z= 0.421 Chirality : 0.053 0.256 2213 Planarity : 0.005 0.047 1473 Dihedral : 34.968 129.685 4104 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -0.37 (0.28), residues: 838 helix: 0.74 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 669 TYR 0.048 0.002 TYR F 98 PHE 0.009 0.001 PHE A 102 TRP 0.006 0.002 TRP E 87 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.18 (13502) covalent geometry : angle 0.73180 / 0.42 (19473) hydrogen bonds : bond 0.07349 / 4.96 ( 745) hydrogen bonds : angle 3.94692 / 2.72 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9465 (m-10) cc_final: 0.8992 (m-10) REVERT: A 66 GLN cc_start: 0.9696 (mm110) cc_final: 0.9303 (mp10) REVERT: A 74 GLU cc_start: 0.9048 (tt0) cc_final: 0.8512 (mt-10) REVERT: A 85 TYR cc_start: 0.9540 (m-80) cc_final: 0.9122 (m-80) REVERT: A 137 GLN cc_start: 0.8912 (mp10) cc_final: 0.8676 (mp10) REVERT: B 59 LYS cc_start: 0.9689 (ptmt) cc_final: 0.9435 (ptmm) REVERT: B 63 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8951 (mt-10) REVERT: B 84 MET cc_start: 0.9044 (mmt) cc_final: 0.8694 (mmm) REVERT: C 36 LYS cc_start: 0.9522 (mtpt) cc_final: 0.9038 (mmtp) REVERT: C 87 ILE cc_start: 0.9752 (mm) cc_final: 0.9420 (tp) REVERT: D 99 ARG cc_start: 0.9356 (mtt180) cc_final: 0.8751 (ttm110) REVERT: E 90 MET cc_start: 0.9193 (tmm) cc_final: 0.8889 (tmm) REVERT: E 97 GLU cc_start: 0.9483 (tt0) cc_final: 0.8847 (tt0) REVERT: E 100 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9055 (mt-10) REVERT: E 128 GLN cc_start: 0.9666 (tt0) cc_final: 0.9416 (tp-100) REVERT: F 59 LYS cc_start: 0.9691 (ptmm) cc_final: 0.9398 (ptmm) REVERT: F 60 VAL cc_start: 0.9576 (m) cc_final: 0.9138 (p) REVERT: F 63 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8999 (mp0) REVERT: F 66 ILE cc_start: 0.9887 (mt) cc_final: 0.9623 (tt) REVERT: F 74 GLU cc_start: 0.9559 (tt0) cc_final: 0.9078 (tm-30) REVERT: F 79 LYS cc_start: 0.9641 (mptt) cc_final: 0.9130 (ttpp) REVERT: G 73 ASN cc_start: 0.9227 (t0) cc_final: 0.8974 (m110) REVERT: G 78 ILE cc_start: 0.9790 (mt) cc_final: 0.9387 (tp) REVERT: G 91 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8680 (mm-30) REVERT: G 95 LYS cc_start: 0.9655 (tttp) cc_final: 0.9406 (tptt) REVERT: H 59 MET cc_start: 0.9057 (tpp) cc_final: 0.8833 (tpp) REVERT: H 68 ASP cc_start: 0.9244 (t70) cc_final: 0.8887 (t0) REVERT: H 71 GLU cc_start: 0.9220 (pp20) cc_final: 0.9003 (pp20) REVERT: H 72 ARG cc_start: 0.9660 (ttm170) cc_final: 0.9194 (ptm160) REVERT: H 80 LEU cc_start: 0.9662 (tp) cc_final: 0.9354 (tp) REVERT: H 99 ARG cc_start: 0.9519 (mtt90) cc_final: 0.8738 (ttm110) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1183 time to fit residues: 30.3783 Evaluate side-chains 137 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 92 optimal weight: 40.0000 chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 96 GLN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.023217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.019467 restraints weight = 169632.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.020260 restraints weight = 82160.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.020802 restraints weight = 49129.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.021177 restraints weight = 32960.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.021444 restraints weight = 23950.370| |-----------------------------------------------------------------------------| r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13502 Z= 0.157 Angle : 0.727 11.665 19473 Z= 0.414 Chirality : 0.052 0.245 2213 Planarity : 0.005 0.047 1473 Dihedral : 34.931 130.374 4104 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.29), residues: 838 helix: 0.90 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.18 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.035 0.002 TYR F 51 PHE 0.018 0.002 PHE C 25 TRP 0.005 0.001 TRP K 668 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (13502) covalent geometry : angle 0.72680 / 0.41 (19473) hydrogen bonds : bond 0.06573 / 4.43 ( 745) hydrogen bonds : angle 3.90229 / 2.71 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9456 (m-10) cc_final: 0.9142 (m-10) REVERT: A 66 GLN cc_start: 0.9694 (mm110) cc_final: 0.9301 (mp10) REVERT: A 74 GLU cc_start: 0.9019 (tt0) cc_final: 0.8479 (mt-10) REVERT: A 85 TYR cc_start: 0.9546 (m-80) cc_final: 0.9107 (m-80) REVERT: A 137 GLN cc_start: 0.8935 (mp10) cc_final: 0.8730 (mp10) REVERT: B 59 LYS cc_start: 0.9730 (ptmt) cc_final: 0.9472 (ptmm) REVERT: B 60 VAL cc_start: 0.9576 (m) cc_final: 0.9182 (p) REVERT: B 63 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8894 (mt-10) REVERT: B 72 TYR cc_start: 0.9718 (m-10) cc_final: 0.9460 (m-80) REVERT: B 84 MET cc_start: 0.9003 (mmt) cc_final: 0.8726 (mmm) REVERT: C 36 LYS cc_start: 0.9505 (mtpt) cc_final: 0.9023 (mmtp) REVERT: C 64 GLU cc_start: 0.9597 (tt0) cc_final: 0.8852 (tt0) REVERT: C 87 ILE cc_start: 0.9742 (mm) cc_final: 0.9409 (tp) REVERT: D 34 LYS cc_start: 0.8331 (mppt) cc_final: 0.8070 (mmtm) REVERT: D 71 GLU cc_start: 0.9281 (pp20) cc_final: 0.8824 (pp20) REVERT: D 99 ARG cc_start: 0.9377 (mtt180) cc_final: 0.8774 (ttm110) REVERT: E 90 MET cc_start: 0.9194 (tmm) cc_final: 0.8877 (tmm) REVERT: E 96 GLN cc_start: 0.9343 (tp40) cc_final: 0.8951 (tp40) REVERT: E 97 GLU cc_start: 0.9460 (tt0) cc_final: 0.8830 (tt0) REVERT: E 100 GLU cc_start: 0.9462 (mt-10) cc_final: 0.9259 (mt-10) REVERT: E 109 ASP cc_start: 0.9186 (m-30) cc_final: 0.8781 (m-30) REVERT: E 128 GLN cc_start: 0.9665 (tt0) cc_final: 0.9397 (tp-100) REVERT: F 66 ILE cc_start: 0.9878 (mt) cc_final: 0.9640 (tt) REVERT: F 74 GLU cc_start: 0.9555 (tt0) cc_final: 0.9062 (tm-30) REVERT: F 79 LYS cc_start: 0.9640 (mptt) cc_final: 0.9133 (ttpp) REVERT: G 36 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8882 (mmmt) REVERT: G 73 ASN cc_start: 0.9251 (t0) cc_final: 0.8967 (m110) REVERT: G 78 ILE cc_start: 0.9788 (mt) cc_final: 0.9412 (tp) REVERT: G 91 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8671 (mm-30) REVERT: G 95 LYS cc_start: 0.9636 (tttp) cc_final: 0.9381 (tptt) REVERT: H 59 MET cc_start: 0.8988 (tpp) cc_final: 0.8703 (tpp) REVERT: H 72 ARG cc_start: 0.9656 (ttm170) cc_final: 0.9225 (ptm160) REVERT: H 80 LEU cc_start: 0.9654 (tp) cc_final: 0.9348 (tp) REVERT: H 99 ARG cc_start: 0.9512 (mtt90) cc_final: 0.8726 (ttm110) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1254 time to fit residues: 32.7270 Evaluate side-chains 138 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 40.0000 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.023305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.019544 restraints weight = 170785.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.020332 restraints weight = 83424.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.020869 restraints weight = 50154.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.021242 restraints weight = 33790.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.021509 restraints weight = 24691.055| |-----------------------------------------------------------------------------| r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13502 Z= 0.158 Angle : 0.715 9.612 19473 Z= 0.409 Chirality : 0.052 0.246 2213 Planarity : 0.005 0.047 1473 Dihedral : 34.869 130.412 4104 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 (0.29), residues: 838 helix: 1.00 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 656 TYR 0.023 0.002 TYR C 57 PHE 0.013 0.001 PHE C 25 TRP 0.005 0.001 TRP L 668 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (13502) covalent geometry : angle 0.71549 / 0.41 (19473) hydrogen bonds : bond 0.06455 / 4.36 ( 745) hydrogen bonds : angle 3.86699 / 2.67 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9446 (m-10) cc_final: 0.9116 (m-10) REVERT: A 66 GLN cc_start: 0.9686 (mm110) cc_final: 0.9297 (mp10) REVERT: A 74 GLU cc_start: 0.9024 (tt0) cc_final: 0.8497 (mt-10) REVERT: A 85 TYR cc_start: 0.9549 (m-80) cc_final: 0.9101 (m-80) REVERT: A 109 ASP cc_start: 0.9207 (m-30) cc_final: 0.8832 (m-30) REVERT: A 126 ASP cc_start: 0.9507 (m-30) cc_final: 0.9297 (m-30) REVERT: A 137 GLN cc_start: 0.8975 (mp10) cc_final: 0.8756 (mp10) REVERT: B 59 LYS cc_start: 0.9740 (ptmt) cc_final: 0.9388 (ptmm) REVERT: B 63 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8933 (mp0) REVERT: B 72 TYR cc_start: 0.9717 (m-10) cc_final: 0.9429 (m-80) REVERT: B 84 MET cc_start: 0.8952 (mmt) cc_final: 0.8671 (mmm) REVERT: C 36 LYS cc_start: 0.9508 (mtpt) cc_final: 0.9012 (mmtp) REVERT: C 87 ILE cc_start: 0.9744 (mm) cc_final: 0.9415 (tp) REVERT: C 102 ILE cc_start: 0.9332 (tp) cc_final: 0.8859 (tp) REVERT: D 34 LYS cc_start: 0.8315 (mppt) cc_final: 0.8049 (mmtm) REVERT: D 71 GLU cc_start: 0.9285 (pp20) cc_final: 0.8826 (pp20) REVERT: D 99 ARG cc_start: 0.9375 (mtt180) cc_final: 0.8781 (ttm110) REVERT: E 74 GLU cc_start: 0.9483 (tt0) cc_final: 0.9248 (pt0) REVERT: E 90 MET cc_start: 0.9195 (tmm) cc_final: 0.8874 (tpt) REVERT: E 96 GLN cc_start: 0.9196 (tp40) cc_final: 0.8960 (tp40) REVERT: E 97 GLU cc_start: 0.9474 (tt0) cc_final: 0.8855 (tt0) REVERT: E 109 ASP cc_start: 0.9157 (m-30) cc_final: 0.8748 (m-30) REVERT: E 128 GLN cc_start: 0.9663 (tt0) cc_final: 0.9404 (mm-40) REVERT: F 66 ILE cc_start: 0.9884 (mt) cc_final: 0.9633 (tt) REVERT: F 74 GLU cc_start: 0.9555 (tt0) cc_final: 0.9051 (tm-30) REVERT: F 79 LYS cc_start: 0.9630 (mptt) cc_final: 0.9106 (ttpp) REVERT: G 73 ASN cc_start: 0.9222 (t0) cc_final: 0.8945 (m110) REVERT: G 78 ILE cc_start: 0.9733 (mt) cc_final: 0.9359 (tp) REVERT: G 91 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8663 (mm-30) REVERT: G 95 LYS cc_start: 0.9623 (tttp) cc_final: 0.9367 (tptt) REVERT: H 59 MET cc_start: 0.8996 (tpp) cc_final: 0.8718 (tpp) REVERT: H 68 ASP cc_start: 0.9222 (t70) cc_final: 0.8788 (t0) REVERT: H 71 GLU cc_start: 0.9164 (pp20) cc_final: 0.8853 (pp20) REVERT: H 72 ARG cc_start: 0.9682 (ttm170) cc_final: 0.9113 (ptm160) REVERT: H 80 LEU cc_start: 0.9659 (tp) cc_final: 0.9371 (tp) REVERT: H 99 ARG cc_start: 0.9518 (mtt90) cc_final: 0.8714 (ttm110) REVERT: K 661 ARG cc_start: 0.8963 (mtm110) cc_final: 0.8754 (mpp80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1243 time to fit residues: 31.7950 Evaluate side-chains 144 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 72 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.022562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.018956 restraints weight = 175073.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.019710 restraints weight = 85888.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.020227 restraints weight = 51702.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.020581 restraints weight = 34908.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.020839 restraints weight = 25585.385| |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13502 Z= 0.224 Angle : 0.771 14.606 19473 Z= 0.435 Chirality : 0.053 0.239 2213 Planarity : 0.005 0.047 1473 Dihedral : 34.850 130.205 4104 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.25 (0.28), residues: 838 helix: 0.78 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.033 0.002 TYR F 51 PHE 0.014 0.002 PHE E 68 TRP 0.008 0.002 TRP E 87 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.22 (13502) covalent geometry : angle 0.77123 / 0.44 (19473) hydrogen bonds : bond 0.08334 / 5.64 ( 745) hydrogen bonds : angle 4.07701 / 2.82 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.9693 (mm110) cc_final: 0.9329 (mp10) REVERT: A 74 GLU cc_start: 0.9033 (tt0) cc_final: 0.8521 (mt-10) REVERT: A 85 TYR cc_start: 0.9557 (m-80) cc_final: 0.9108 (m-80) REVERT: A 97 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9277 (mt-10) REVERT: B 59 LYS cc_start: 0.9755 (ptmt) cc_final: 0.9416 (ptmm) REVERT: B 63 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8942 (mp0) REVERT: B 72 TYR cc_start: 0.9739 (m-10) cc_final: 0.9470 (m-80) REVERT: B 84 MET cc_start: 0.8954 (mmt) cc_final: 0.8668 (mmm) REVERT: C 36 LYS cc_start: 0.9538 (mtpt) cc_final: 0.9064 (mmtp) REVERT: C 102 ILE cc_start: 0.9366 (tp) cc_final: 0.8909 (tp) REVERT: D 71 GLU cc_start: 0.9284 (pp20) cc_final: 0.8837 (pp20) REVERT: D 99 ARG cc_start: 0.9387 (mtt180) cc_final: 0.8789 (ttm110) REVERT: E 52 ILE cc_start: 0.9621 (mt) cc_final: 0.9376 (mt) REVERT: E 74 GLU cc_start: 0.9471 (tt0) cc_final: 0.9247 (pt0) REVERT: E 90 MET cc_start: 0.9226 (tmm) cc_final: 0.8905 (tpt) REVERT: E 96 GLN cc_start: 0.9119 (tp40) cc_final: 0.8604 (tp40) REVERT: E 97 GLU cc_start: 0.9472 (tt0) cc_final: 0.8872 (tt0) REVERT: E 100 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9104 (mt-10) REVERT: E 128 GLN cc_start: 0.9663 (tt0) cc_final: 0.9433 (tp-100) REVERT: F 59 LYS cc_start: 0.9728 (ptmm) cc_final: 0.9387 (ptmm) REVERT: F 63 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8956 (mp0) REVERT: F 66 ILE cc_start: 0.9887 (mt) cc_final: 0.9660 (tt) REVERT: F 74 GLU cc_start: 0.9592 (tt0) cc_final: 0.9144 (tm-30) REVERT: F 79 LYS cc_start: 0.9654 (mptt) cc_final: 0.9125 (ttpp) REVERT: G 36 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8936 (mmmt) REVERT: G 73 ASN cc_start: 0.9243 (t0) cc_final: 0.8992 (m110) REVERT: G 78 ILE cc_start: 0.9741 (mt) cc_final: 0.9400 (tp) REVERT: G 91 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8734 (mm-30) REVERT: G 95 LYS cc_start: 0.9629 (tttp) cc_final: 0.9375 (tptt) REVERT: H 59 MET cc_start: 0.8886 (tpp) cc_final: 0.8611 (tpp) REVERT: H 80 LEU cc_start: 0.9704 (tp) cc_final: 0.9440 (tp) REVERT: H 99 ARG cc_start: 0.9466 (mtt90) cc_final: 0.8691 (ttm110) REVERT: K 661 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8659 (mpp80) REVERT: L 659 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8019 (ttp80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1276 time to fit residues: 30.8767 Evaluate side-chains 129 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.023258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.019530 restraints weight = 173589.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.020307 restraints weight = 84264.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.020843 restraints weight = 50562.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.021211 restraints weight = 33983.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.021467 restraints weight = 24813.232| |-----------------------------------------------------------------------------| r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13502 Z= 0.156 Angle : 0.734 12.165 19473 Z= 0.415 Chirality : 0.052 0.243 2213 Planarity : 0.005 0.067 1473 Dihedral : 34.896 131.387 4104 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.29), residues: 838 helix: 0.88 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.92 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 656 TYR 0.028 0.002 TYR F 51 PHE 0.011 0.001 PHE C 25 TRP 0.005 0.001 TRP E 87 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (13502) covalent geometry : angle 0.73430 / 0.41 (19473) hydrogen bonds : bond 0.06307 / 4.26 ( 745) hydrogen bonds : angle 3.92137 / 2.71 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.9688 (mm110) cc_final: 0.9310 (mp10) REVERT: A 74 GLU cc_start: 0.8965 (tt0) cc_final: 0.8452 (mt-10) REVERT: A 85 TYR cc_start: 0.9555 (m-80) cc_final: 0.9103 (m-80) REVERT: A 97 GLU cc_start: 0.9493 (mt-10) cc_final: 0.8979 (mt-10) REVERT: A 100 GLU cc_start: 0.9518 (mt-10) cc_final: 0.8966 (mt-10) REVERT: A 109 ASP cc_start: 0.9209 (m-30) cc_final: 0.8828 (m-30) REVERT: A 126 ASP cc_start: 0.9472 (m-30) cc_final: 0.9258 (m-30) REVERT: B 59 LYS cc_start: 0.9753 (ptmt) cc_final: 0.9426 (ptmm) REVERT: B 63 GLU cc_start: 0.9433 (mt-10) cc_final: 0.8898 (mp0) REVERT: B 72 TYR cc_start: 0.9727 (m-10) cc_final: 0.9465 (m-80) REVERT: B 84 MET cc_start: 0.8917 (mmt) cc_final: 0.8628 (mmm) REVERT: C 36 LYS cc_start: 0.9516 (mtpt) cc_final: 0.9039 (mmtp) REVERT: C 102 ILE cc_start: 0.9349 (tp) cc_final: 0.8888 (tp) REVERT: D 34 LYS cc_start: 0.8349 (mppt) cc_final: 0.8102 (mmtm) REVERT: D 99 ARG cc_start: 0.9379 (mtt180) cc_final: 0.8780 (ttm110) REVERT: E 52 ILE cc_start: 0.9610 (mt) cc_final: 0.9356 (mt) REVERT: E 68 PHE cc_start: 0.9542 (t80) cc_final: 0.9310 (t80) REVERT: E 74 GLU cc_start: 0.9466 (tt0) cc_final: 0.9202 (pt0) REVERT: E 79 PHE cc_start: 0.8259 (m-80) cc_final: 0.7441 (m-80) REVERT: E 85 TYR cc_start: 0.9460 (m-10) cc_final: 0.8969 (m-80) REVERT: E 90 MET cc_start: 0.9185 (tmm) cc_final: 0.8826 (tpt) REVERT: E 97 GLU cc_start: 0.9443 (tt0) cc_final: 0.8839 (tt0) REVERT: E 128 GLN cc_start: 0.9649 (tt0) cc_final: 0.9437 (mm-40) REVERT: F 63 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9194 (tp30) REVERT: F 66 ILE cc_start: 0.9878 (mt) cc_final: 0.9635 (tt) REVERT: F 74 GLU cc_start: 0.9561 (tt0) cc_final: 0.9103 (tm-30) REVERT: F 79 LYS cc_start: 0.9641 (mptt) cc_final: 0.9177 (ttpp) REVERT: G 73 ASN cc_start: 0.9235 (t0) cc_final: 0.8969 (m110) REVERT: G 78 ILE cc_start: 0.9724 (mt) cc_final: 0.9362 (tp) REVERT: G 91 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8644 (mm-30) REVERT: G 95 LYS cc_start: 0.9607 (tttp) cc_final: 0.9348 (tptt) REVERT: H 59 MET cc_start: 0.8892 (tpp) cc_final: 0.8592 (tpp) REVERT: H 80 LEU cc_start: 0.9639 (tp) cc_final: 0.9330 (tp) REVERT: H 99 ARG cc_start: 0.9486 (mtt90) cc_final: 0.8695 (ttm110) REVERT: K 661 ARG cc_start: 0.8950 (mtm110) cc_final: 0.8629 (mpp80) REVERT: L 656 ARG cc_start: 0.8668 (mmp80) cc_final: 0.7922 (mmm160) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1218 time to fit residues: 30.7452 Evaluate side-chains 140 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.023254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.019518 restraints weight = 174830.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.020291 restraints weight = 85362.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.020824 restraints weight = 51306.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.021186 restraints weight = 34530.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.021451 restraints weight = 25314.674| |-----------------------------------------------------------------------------| r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13502 Z= 0.165 Angle : 0.722 9.585 19473 Z= 0.410 Chirality : 0.051 0.241 2213 Planarity : 0.005 0.047 1473 Dihedral : 34.837 130.895 4104 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 838 helix: 0.98 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 656 TYR 0.025 0.001 TYR F 51 PHE 0.020 0.002 PHE E 68 TRP 0.006 0.002 TRP L 668 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (13502) covalent geometry : angle 0.72226 / 0.41 (19473) hydrogen bonds : bond 0.06646 / 4.51 ( 745) hydrogen bonds : angle 3.90436 / 2.70 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.9692 (mm110) cc_final: 0.9326 (mp10) REVERT: A 74 GLU cc_start: 0.8970 (tt0) cc_final: 0.8445 (mt-10) REVERT: A 85 TYR cc_start: 0.9558 (m-80) cc_final: 0.9097 (m-80) REVERT: A 97 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9234 (mt-10) REVERT: A 109 ASP cc_start: 0.9180 (m-30) cc_final: 0.8816 (m-30) REVERT: A 126 ASP cc_start: 0.9474 (m-30) cc_final: 0.9253 (m-30) REVERT: A 137 GLN cc_start: 0.9000 (mp10) cc_final: 0.8783 (mp10) REVERT: B 59 LYS cc_start: 0.9753 (ptmt) cc_final: 0.9451 (ptmm) REVERT: B 63 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8891 (mp0) REVERT: B 72 TYR cc_start: 0.9735 (m-10) cc_final: 0.9478 (m-80) REVERT: B 84 MET cc_start: 0.8891 (mmt) cc_final: 0.8602 (mmm) REVERT: C 36 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9085 (mmtp) REVERT: C 102 ILE cc_start: 0.9329 (tp) cc_final: 0.8869 (tp) REVERT: D 34 LYS cc_start: 0.8289 (mppt) cc_final: 0.8018 (mmtm) REVERT: D 99 ARG cc_start: 0.9372 (mtt180) cc_final: 0.8815 (ttm110) REVERT: E 52 ILE cc_start: 0.9607 (mt) cc_final: 0.9216 (mt) REVERT: E 79 PHE cc_start: 0.8325 (m-80) cc_final: 0.7529 (m-80) REVERT: E 85 TYR cc_start: 0.9469 (m-10) cc_final: 0.8948 (m-80) REVERT: E 90 MET cc_start: 0.9187 (tmm) cc_final: 0.8845 (tpt) REVERT: E 128 GLN cc_start: 0.9640 (tt0) cc_final: 0.9436 (mm-40) REVERT: F 63 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9155 (tp30) REVERT: F 66 ILE cc_start: 0.9890 (mt) cc_final: 0.9623 (tt) REVERT: F 74 GLU cc_start: 0.9570 (tt0) cc_final: 0.9123 (tm-30) REVERT: F 79 LYS cc_start: 0.9646 (mptt) cc_final: 0.9184 (ttpp) REVERT: G 73 ASN cc_start: 0.9235 (t0) cc_final: 0.8969 (m110) REVERT: G 78 ILE cc_start: 0.9716 (mt) cc_final: 0.9374 (tp) REVERT: G 91 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8685 (mm-30) REVERT: G 95 LYS cc_start: 0.9604 (tttp) cc_final: 0.9339 (tptt) REVERT: H 59 MET cc_start: 0.8885 (tpp) cc_final: 0.8561 (tpp) REVERT: H 68 ASP cc_start: 0.9146 (t70) cc_final: 0.8804 (t0) REVERT: H 72 ARG cc_start: 0.9670 (ttm170) cc_final: 0.9091 (ptm160) REVERT: H 80 LEU cc_start: 0.9660 (tp) cc_final: 0.9373 (tp) REVERT: H 99 ARG cc_start: 0.9494 (mtt90) cc_final: 0.8707 (ttm110) REVERT: K 661 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8624 (mpp80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1316 time to fit residues: 32.9081 Evaluate side-chains 143 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 40.0000 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 40.0000 chunk 89 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 95 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.022648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.018999 restraints weight = 179302.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.019759 restraints weight = 86793.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.020274 restraints weight = 51995.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.020627 restraints weight = 35058.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.020880 restraints weight = 25770.512| |-----------------------------------------------------------------------------| r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13502 Z= 0.215 Angle : 0.761 14.509 19473 Z= 0.427 Chirality : 0.052 0.236 2213 Planarity : 0.005 0.046 1473 Dihedral : 34.858 131.038 4104 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 838 helix: 0.82 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 656 TYR 0.024 0.002 TYR F 51 PHE 0.016 0.002 PHE E 68 TRP 0.009 0.002 TRP E 87 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.22 (13502) covalent geometry : angle 0.76123 / 0.43 (19473) hydrogen bonds : bond 0.08022 / 5.44 ( 745) hydrogen bonds : angle 4.05076 / 2.81 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.02 seconds wall clock time: 29 minutes 37.15 seconds (1777.15 seconds total)