Starting phenix.real_space_refine on Thu Aug 6 07:51:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7j_38100/08_2026/8x7j_38100.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1025 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 288 5.49 5 S 25 5.16 5 C 7736 2.51 5 N 2547 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2967 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2937 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "K" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1031 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 126} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 405 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 399 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13064 SG CYS L 31 59.328 67.509 25.982 1.00218.04 S ATOM 13203 SG CYS L 51 60.840 71.001 26.041 1.00210.14 S ATOM 13227 SG CYS L 54 57.120 70.534 25.078 1.00213.50 S ATOM 12959 SG CYS L 16 71.165 67.606 21.224 1.00283.03 S ATOM 12977 SG CYS L 19 74.736 68.117 20.046 1.00282.47 S ATOM 13100 SG CYS L 36 74.096 65.680 22.767 1.00253.66 S ATOM 13118 SG CYS L 39 73.702 69.387 23.482 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 13739 At special positions: 0 Unit cell: (118.14, 125.658, 112.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 25 16.00 P 288 15.00 O 3141 8.00 N 2547 7.00 C 7736 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: 1.19 Conformation dependent library (CDL) restraints added in 449.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " Number of angles added : 9 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1918 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 63.1% alpha, 4.4% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.515A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.870A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.472A 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 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.310A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 removed outlier: 4.026A pdb=" N ASN F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.886A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.730A 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 73 removed outlier: 4.526A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.859A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.965A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.940A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.911A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 32 through 38 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6 removed outlier: 5.969A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 478 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3179 1.34 - 1.45: 4115 1.45 - 1.57: 6668 1.57 - 1.69: 574 1.69 - 1.81: 38 Bond restraints: 14574 Sorted by residual: bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC J 21 " pdb=" C2' DC J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 18682 1.04 - 2.08: 1694 2.08 - 3.13: 548 3.13 - 4.17: 31 4.17 - 5.21: 9 Bond angle restraints: 20964 Sorted by residual: angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.78e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I -59 " pdb=" C4 DT I -59 " pdb=" O4 DT I -59 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 71 " pdb=" C4 DT J 71 " pdb=" O4 DT J 71 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 20959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6717 35.75 - 71.50: 1268 71.50 - 107.25: 20 107.25 - 143.01: 1 143.01 - 178.76: 2 Dihedral angle restraints: 8008 sinusoidal: 5051 harmonic: 2957 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual -140.00 38.76 -178.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 53.55 166.45 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 83.64 136.36 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1514 0.035 - 0.070: 625 0.070 - 0.105: 224 0.105 - 0.140: 46 0.140 - 0.175: 1 Chirality restraints: 2410 Sorted by residual: chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2407 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.020 2.00e-02 2.50e+03 8.19e-03 2.01e+00 pdb=" N9 DG I 48 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO H 103 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 8 " -0.017 2.00e-02 2.50e+03 7.87e-03 1.86e+00 pdb=" N9 DG I 8 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 8 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 8 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 8 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 8 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 8 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 8 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG I 8 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 104 2.49 - 3.09: 9046 3.09 - 3.69: 24450 3.69 - 4.30: 34292 4.30 - 4.90: 50522 Nonbonded interactions: 118414 Sorted by model distance: nonbonded pdb=" SG CYS L 54 " pdb=" CD ARG L 56 " model vdw 1.882 3.800 nonbonded pdb=" N2 DG I 56 " pdb=" O2 DC J -56 " model vdw 2.048 2.496 nonbonded pdb=" N2 DG I -42 " pdb=" O2 DC J 42 " model vdw 2.069 2.496 nonbonded pdb=" O2 DC I 52 " pdb=" N2 DG J -52 " model vdw 2.082 2.496 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.095 2.496 ... (remaining 118409 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' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 11 through 14 or resid 16 through 117)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.005 0.037 14582 Z= 0.478 Angle : 0.679 5.210 20973 Z= 0.606 Chirality : 0.043 0.175 2410 Planarity : 0.003 0.034 1663 Dihedral : 25.848 178.758 6090 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.73 % Allowed : 4.46 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.28), residues: 988 helix: 2.81 (0.21), residues: 636 sheet: -0.95 (0.96), residues: 28 loop : -0.35 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 42 TYR 0.008 0.001 TYR F 72 PHE 0.008 0.001 PHE E 67 TRP 0.005 0.001 TRP K 93 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.48 (14574) covalent geometry : angle 0.67866 / 0.61 (20964) hydrogen bonds : bond 0.12179 / 8.63 ( 823) hydrogen bonds : angle 3.69416 / 2.54 ( 2018) metal coordination : bond 0.00815 / 0.46 ( 8) metal coordination : angle 1.56213 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.385 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: B 49 LEU cc_start: 0.9256 (mt) cc_final: 0.8300 (mp) REVERT: C 56 GLU cc_start: 0.8368 (tt0) cc_final: 0.8106 (tt0) REVERT: C 68 ASN cc_start: 0.8931 (m-40) cc_final: 0.7374 (m-40) REVERT: D 68 ASP cc_start: 0.8713 (t70) cc_final: 0.8399 (t0) REVERT: E 73 GLU cc_start: 0.7680 (tt0) cc_final: 0.7463 (tt0) REVERT: E 94 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8131 (mm-30) REVERT: G 56 GLU cc_start: 0.8579 (tt0) cc_final: 0.8331 (tt0) REVERT: G 68 ASN cc_start: 0.8179 (m-40) cc_final: 0.7725 (m-40) REVERT: H 62 MET cc_start: 0.9329 (mmm) cc_final: 0.8972 (mmt) REVERT: H 68 ASP cc_start: 0.8817 (t70) cc_final: 0.8577 (t0) REVERT: K 92 GLN cc_start: 0.9289 (tp-100) cc_final: 0.8958 (tp-100) REVERT: K 147 MET cc_start: 0.7873 (mtt) cc_final: 0.7046 (mtt) outliers start: 14 outliers final: 8 residues processed: 263 average time/residue: 0.1291 time to fit residues: 46.5286 Evaluate side-chains 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 64 ASN D 47 GLN D 82 HIS ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.059697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039901 restraints weight = 84422.940| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.44 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14582 Z= 0.236 Angle : 0.699 13.955 20973 Z= 0.399 Chirality : 0.045 0.315 2410 Planarity : 0.005 0.037 1663 Dihedral : 30.100 179.097 4274 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.97 % Allowed : 12.02 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.27), residues: 988 helix: 2.46 (0.21), residues: 643 sheet: 0.05 (1.19), residues: 23 loop : -0.51 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 129 TYR 0.033 0.002 TYR D 83 PHE 0.010 0.001 PHE C 25 TRP 0.007 0.002 TRP K 33 HIS 0.005 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (14574) covalent geometry : angle 0.69404 / 0.40 (20964) hydrogen bonds : bond 0.09311 / 6.44 ( 823) hydrogen bonds : angle 3.56878 / 2.51 ( 2018) metal coordination : bond 0.02655 / 1.62 ( 8) metal coordination : angle 4.01193 / 2.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8727 (mt0) cc_final: 0.8521 (mt0) REVERT: B 49 LEU cc_start: 0.9330 (mt) cc_final: 0.8891 (mp) REVERT: C 56 GLU cc_start: 0.8573 (tt0) cc_final: 0.8271 (tt0) REVERT: C 68 ASN cc_start: 0.8609 (m-40) cc_final: 0.8324 (m-40) REVERT: D 68 ASP cc_start: 0.8988 (t70) cc_final: 0.8679 (t0) REVERT: E 94 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8341 (mm-30) REVERT: G 38 ASN cc_start: 0.7298 (t0) cc_final: 0.6891 (t0) REVERT: G 56 GLU cc_start: 0.8857 (tt0) cc_final: 0.8398 (tt0) REVERT: H 62 MET cc_start: 0.9561 (mmm) cc_final: 0.9159 (mmt) REVERT: H 68 ASP cc_start: 0.9151 (t70) cc_final: 0.8820 (t0) REVERT: H 113 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8681 (mt-10) REVERT: K 92 GLN cc_start: 0.9248 (tp-100) cc_final: 0.9029 (tm-30) REVERT: K 147 MET cc_start: 0.7916 (mtt) cc_final: 0.7055 (mtt) REVERT: L 42 SER cc_start: 0.8090 (m) cc_final: 0.7890 (p) outliers start: 24 outliers final: 16 residues processed: 185 average time/residue: 0.1120 time to fit residues: 29.8122 Evaluate side-chains 175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN B 75 HIS D 109 HIS G 24 GLN G 104 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.060062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040307 restraints weight = 84397.445| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.42 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14582 Z= 0.161 Angle : 0.621 9.914 20973 Z= 0.367 Chirality : 0.042 0.320 2410 Planarity : 0.004 0.048 1663 Dihedral : 30.092 178.077 4266 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.11 % Allowed : 13.14 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 988 helix: 2.52 (0.21), residues: 643 sheet: 0.07 (1.17), residues: 23 loop : -0.56 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 56 TYR 0.033 0.002 TYR D 83 PHE 0.008 0.001 PHE F 61 TRP 0.007 0.001 TRP K 93 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (14574) covalent geometry : angle 0.61655 / 0.37 (20964) hydrogen bonds : bond 0.08506 / 5.79 ( 823) hydrogen bonds : angle 3.35014 / 2.35 ( 2018) metal coordination : bond 0.01305 / 0.69 ( 8) metal coordination : angle 3.60313 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8406 (mt-10) REVERT: C 56 GLU cc_start: 0.8584 (tt0) cc_final: 0.8280 (tt0) REVERT: C 64 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 68 ASN cc_start: 0.8608 (m-40) cc_final: 0.8309 (m-40) REVERT: D 68 ASP cc_start: 0.9005 (t70) cc_final: 0.8709 (t0) REVERT: E 94 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8239 (mt-10) REVERT: E 133 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7866 (mt-10) REVERT: G 38 ASN cc_start: 0.7361 (t0) cc_final: 0.6859 (t0) REVERT: G 56 GLU cc_start: 0.8853 (tt0) cc_final: 0.8343 (tt0) REVERT: H 51 ASP cc_start: 0.8343 (p0) cc_final: 0.8085 (p0) REVERT: H 62 MET cc_start: 0.9542 (mmm) cc_final: 0.9152 (mmt) REVERT: H 68 ASP cc_start: 0.9164 (t70) cc_final: 0.8835 (t0) REVERT: H 79 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: H 113 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8676 (mt-10) REVERT: K 147 MET cc_start: 0.7870 (mtt) cc_final: 0.6998 (mtt) REVERT: L 42 SER cc_start: 0.8100 (m) cc_final: 0.7891 (p) REVERT: M 1 MET cc_start: 0.7315 (ppp) cc_final: 0.6533 (ppp) REVERT: M 18 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8174 (tm-30) outliers start: 17 outliers final: 14 residues processed: 186 average time/residue: 0.0903 time to fit residues: 24.7134 Evaluate side-chains 176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 88 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 119 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN K 7 ASN ** L 33 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 = 0.3630 r_free = 0.3630 target = 0.058450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038580 restraints weight = 85307.652| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.36 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14582 Z= 0.269 Angle : 0.694 9.090 20973 Z= 0.396 Chirality : 0.044 0.317 2410 Planarity : 0.004 0.043 1663 Dihedral : 30.254 178.807 4266 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.22 % Allowed : 13.26 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 1.92 (0.27), residues: 988 helix: 2.23 (0.21), residues: 646 sheet: -0.24 (1.15), residues: 23 loop : -0.65 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 20 TYR 0.043 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP K 93 HIS 0.005 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.27 (14574) covalent geometry : angle 0.69099 / 0.40 (20964) hydrogen bonds : bond 0.09170 / 6.39 ( 823) hydrogen bonds : angle 3.64644 / 2.59 ( 2018) metal coordination : bond 0.01366 / 0.76 ( 8) metal coordination : angle 3.36431 / 2.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8058 (mt-10) REVERT: C 56 GLU cc_start: 0.8601 (tt0) cc_final: 0.8308 (tt0) REVERT: C 64 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 68 ASN cc_start: 0.8812 (m-40) cc_final: 0.8355 (m-40) REVERT: D 68 ASP cc_start: 0.9118 (t70) cc_final: 0.8751 (t0) REVERT: E 133 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 38 ASN cc_start: 0.7559 (t0) cc_final: 0.7179 (t0) REVERT: G 56 GLU cc_start: 0.8898 (tt0) cc_final: 0.8318 (tt0) REVERT: H 37 TYR cc_start: 0.9080 (m-80) cc_final: 0.8582 (m-80) REVERT: H 68 ASP cc_start: 0.9160 (t70) cc_final: 0.8872 (t0) REVERT: H 113 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8720 (mt-10) REVERT: K 89 LEU cc_start: 0.9239 (mt) cc_final: 0.8918 (tp) REVERT: L 42 SER cc_start: 0.7876 (m) cc_final: 0.7665 (p) REVERT: M 1 MET cc_start: 0.7117 (ppp) cc_final: 0.6706 (ppp) outliers start: 26 outliers final: 21 residues processed: 177 average time/residue: 0.1065 time to fit residues: 27.5524 Evaluate side-chains 176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.059668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039867 restraints weight = 83997.066| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.39 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14582 Z= 0.145 Angle : 0.613 10.006 20973 Z= 0.362 Chirality : 0.043 0.333 2410 Planarity : 0.004 0.063 1663 Dihedral : 30.155 178.328 4266 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.60 % Allowed : 14.37 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.28), residues: 988 helix: 2.42 (0.21), residues: 647 sheet: -1.01 (0.98), residues: 28 loop : -0.55 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.026 0.001 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP K 141 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (14574) covalent geometry : angle 0.61004 / 0.36 (20964) hydrogen bonds : bond 0.08363 / 5.63 ( 823) hydrogen bonds : angle 3.30657 / 2.34 ( 2018) metal coordination : bond 0.01061 / 0.59 ( 8) metal coordination : angle 2.84185 / 2.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8429 (mt-10) REVERT: C 56 GLU cc_start: 0.8581 (tt0) cc_final: 0.8277 (tt0) REVERT: C 64 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 68 ASN cc_start: 0.8740 (m-40) cc_final: 0.8224 (m-40) REVERT: D 63 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8674 (m-40) REVERT: D 68 ASP cc_start: 0.9037 (t70) cc_final: 0.8755 (t0) REVERT: D 79 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8554 (ttp-110) REVERT: E 94 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8337 (mt-10) REVERT: E 133 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7899 (mt-10) REVERT: F 22 LEU cc_start: 0.8059 (pt) cc_final: 0.7737 (tt) REVERT: G 38 ASN cc_start: 0.7582 (t0) cc_final: 0.7179 (t0) REVERT: G 56 GLU cc_start: 0.8875 (tt0) cc_final: 0.8354 (tt0) REVERT: G 89 ASN cc_start: 0.9026 (m-40) cc_final: 0.8752 (m-40) REVERT: G 92 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8797 (mt-10) REVERT: H 37 TYR cc_start: 0.9072 (m-80) cc_final: 0.8702 (m-80) REVERT: H 68 ASP cc_start: 0.9140 (t70) cc_final: 0.8836 (t0) REVERT: H 76 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8430 (mm-30) REVERT: H 79 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: K 89 LEU cc_start: 0.9153 (mt) cc_final: 0.8882 (tp) REVERT: L 20 MET cc_start: 0.7461 (mmt) cc_final: 0.7072 (mpp) REVERT: L 42 SER cc_start: 0.7888 (m) cc_final: 0.7675 (p) REVERT: M 1 MET cc_start: 0.6603 (ppp) cc_final: 0.6234 (mtp) outliers start: 21 outliers final: 17 residues processed: 186 average time/residue: 0.0996 time to fit residues: 27.2672 Evaluate side-chains 180 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.059730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039844 restraints weight = 84011.903| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.38 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14582 Z= 0.149 Angle : 0.613 9.063 20973 Z= 0.362 Chirality : 0.042 0.316 2410 Planarity : 0.004 0.063 1663 Dihedral : 30.107 179.250 4266 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.73 % Allowed : 15.49 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.28), residues: 988 helix: 2.48 (0.21), residues: 645 sheet: -0.96 (0.99), residues: 28 loop : -0.58 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.019 0.001 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.003 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (14574) covalent geometry : angle 0.61051 / 0.36 (20964) hydrogen bonds : bond 0.08298 / 5.60 ( 823) hydrogen bonds : angle 3.26761 / 2.31 ( 2018) metal coordination : bond 0.00955 / 0.52 ( 8) metal coordination : angle 2.52333 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 77 LYS cc_start: 0.9310 (mtmm) cc_final: 0.8844 (mtmm) REVERT: C 56 GLU cc_start: 0.8559 (tt0) cc_final: 0.8285 (tt0) REVERT: C 64 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 68 ASN cc_start: 0.8725 (m-40) cc_final: 0.8169 (m-40) REVERT: D 63 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8676 (m-40) REVERT: D 68 ASP cc_start: 0.9024 (t70) cc_final: 0.8744 (t0) REVERT: D 79 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8546 (ttp-110) REVERT: E 94 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8273 (mt-10) REVERT: E 133 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7896 (mt-10) REVERT: F 22 LEU cc_start: 0.8103 (pt) cc_final: 0.7806 (tt) REVERT: G 38 ASN cc_start: 0.7615 (t0) cc_final: 0.7219 (t0) REVERT: G 56 GLU cc_start: 0.8844 (tt0) cc_final: 0.8336 (tt0) REVERT: G 89 ASN cc_start: 0.9020 (m-40) cc_final: 0.8748 (m-40) REVERT: G 92 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8816 (mt-10) REVERT: H 37 TYR cc_start: 0.9088 (m-80) cc_final: 0.8713 (m-80) REVERT: H 68 ASP cc_start: 0.9133 (t70) cc_final: 0.8816 (t0) REVERT: H 76 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8398 (mm-30) REVERT: H 79 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7900 (mtm-85) REVERT: K 89 LEU cc_start: 0.9194 (mt) cc_final: 0.8888 (tp) REVERT: L 20 MET cc_start: 0.7445 (mmt) cc_final: 0.7082 (mpp) REVERT: L 42 SER cc_start: 0.7889 (m) cc_final: 0.7681 (p) outliers start: 22 outliers final: 19 residues processed: 181 average time/residue: 0.1026 time to fit residues: 27.3652 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.059677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.039815 restraints weight = 84808.937| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.40 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14582 Z= 0.158 Angle : 0.612 8.763 20973 Z= 0.360 Chirality : 0.042 0.312 2410 Planarity : 0.004 0.054 1663 Dihedral : 30.094 179.142 4266 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.35 % Allowed : 16.48 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.28), residues: 988 helix: 2.48 (0.21), residues: 646 sheet: -0.95 (1.00), residues: 28 loop : -0.54 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.017 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 TRP 0.003 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (14574) covalent geometry : angle 0.61026 / 0.36 (20964) hydrogen bonds : bond 0.08240 / 5.57 ( 823) hydrogen bonds : angle 3.21382 / 2.28 ( 2018) metal coordination : bond 0.00851 / 0.48 ( 8) metal coordination : angle 2.53215 / 2.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8440 (mt-10) REVERT: C 56 GLU cc_start: 0.8560 (tt0) cc_final: 0.8281 (tt0) REVERT: C 64 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 68 ASN cc_start: 0.8739 (m-40) cc_final: 0.8114 (m-40) REVERT: D 63 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: D 68 ASP cc_start: 0.9035 (t70) cc_final: 0.8756 (t0) REVERT: E 94 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8339 (mt-10) REVERT: E 133 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7901 (mt-10) REVERT: F 22 LEU cc_start: 0.8100 (pt) cc_final: 0.7815 (tt) REVERT: G 38 ASN cc_start: 0.7307 (t0) cc_final: 0.6993 (t0) REVERT: G 56 GLU cc_start: 0.8863 (tt0) cc_final: 0.8279 (tt0) REVERT: G 89 ASN cc_start: 0.9023 (m-40) cc_final: 0.8730 (m-40) REVERT: G 92 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8818 (mt-10) REVERT: H 37 TYR cc_start: 0.9123 (m-80) cc_final: 0.8752 (m-80) REVERT: H 68 ASP cc_start: 0.9127 (t70) cc_final: 0.8832 (t0) REVERT: H 76 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8408 (mm-30) REVERT: H 79 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8132 (mtm-85) REVERT: K 89 LEU cc_start: 0.9199 (mt) cc_final: 0.8894 (tp) REVERT: L 20 MET cc_start: 0.7558 (mmt) cc_final: 0.7206 (mpp) REVERT: L 42 SER cc_start: 0.7940 (m) cc_final: 0.7723 (p) REVERT: M 1 MET cc_start: 0.6148 (mtp) cc_final: 0.4451 (pmm) outliers start: 19 outliers final: 17 residues processed: 179 average time/residue: 0.1031 time to fit residues: 27.3120 Evaluate side-chains 182 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.060155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040288 restraints weight = 84318.778| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.38 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14582 Z= 0.139 Angle : 0.608 8.354 20973 Z= 0.359 Chirality : 0.042 0.311 2410 Planarity : 0.004 0.062 1663 Dihedral : 30.022 179.018 4265 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.73 % Allowed : 17.10 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.28), residues: 988 helix: 2.47 (0.21), residues: 647 sheet: -0.89 (0.99), residues: 28 loop : -0.50 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.016 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP K 141 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14574) covalent geometry : angle 0.60684 / 0.36 (20964) hydrogen bonds : bond 0.08274 / 5.55 ( 823) hydrogen bonds : angle 3.14023 / 2.23 ( 2018) metal coordination : bond 0.00710 / 0.40 ( 8) metal coordination : angle 2.24233 / 1.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8414 (mt-10) REVERT: C 56 GLU cc_start: 0.8549 (tt0) cc_final: 0.8281 (tt0) REVERT: C 64 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8179 (tm-30) REVERT: D 63 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8596 (m-40) REVERT: D 68 ASP cc_start: 0.9019 (t70) cc_final: 0.8739 (t0) REVERT: E 94 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8282 (mt-10) REVERT: E 133 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7838 (mt-10) REVERT: F 22 LEU cc_start: 0.8165 (pt) cc_final: 0.7899 (tt) REVERT: G 38 ASN cc_start: 0.7336 (t0) cc_final: 0.7064 (t0) REVERT: G 56 GLU cc_start: 0.8829 (tt0) cc_final: 0.8327 (tt0) REVERT: G 89 ASN cc_start: 0.9127 (m-40) cc_final: 0.8884 (m-40) REVERT: G 92 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8696 (mt-10) REVERT: H 37 TYR cc_start: 0.9119 (m-80) cc_final: 0.8766 (m-80) REVERT: H 68 ASP cc_start: 0.9084 (t70) cc_final: 0.8776 (t0) REVERT: H 76 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8396 (mm-30) REVERT: H 79 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8107 (mtm-85) REVERT: K 89 LEU cc_start: 0.9230 (mt) cc_final: 0.8901 (tp) REVERT: L 20 MET cc_start: 0.7512 (mmt) cc_final: 0.7148 (mpp) REVERT: L 42 SER cc_start: 0.7941 (m) cc_final: 0.7721 (p) REVERT: M 1 MET cc_start: 0.6305 (mtp) cc_final: 0.4269 (ppp) outliers start: 22 outliers final: 17 residues processed: 183 average time/residue: 0.1027 time to fit residues: 27.9475 Evaluate side-chains 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 7 ASN ** L 33 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 = 0.3657 r_free = 0.3657 target = 0.059743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039876 restraints weight = 84522.875| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.41 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14582 Z= 0.168 Angle : 0.618 8.130 20973 Z= 0.361 Chirality : 0.041 0.305 2410 Planarity : 0.004 0.059 1663 Dihedral : 30.031 179.031 4265 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.73 % Allowed : 17.22 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.28), residues: 988 helix: 2.44 (0.21), residues: 647 sheet: -0.88 (1.00), residues: 28 loop : -0.54 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.018 0.001 TYR F 88 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (14574) covalent geometry : angle 0.61568 / 0.36 (20964) hydrogen bonds : bond 0.08196 / 5.54 ( 823) hydrogen bonds : angle 3.20526 / 2.28 ( 2018) metal coordination : bond 0.00696 / 0.41 ( 8) metal coordination : angle 2.38743 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9252 (mt) cc_final: 0.9003 (mp) REVERT: C 56 GLU cc_start: 0.8592 (tt0) cc_final: 0.8301 (tt0) REVERT: C 64 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 95 LYS cc_start: 0.9124 (tptt) cc_final: 0.8729 (tppt) REVERT: D 63 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: D 68 ASP cc_start: 0.9040 (t70) cc_final: 0.8766 (t0) REVERT: E 94 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8336 (mt-10) REVERT: E 133 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 22 LEU cc_start: 0.8172 (pt) cc_final: 0.7904 (tt) REVERT: G 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8354 (tt0) REVERT: G 89 ASN cc_start: 0.9100 (m-40) cc_final: 0.8849 (m-40) REVERT: G 92 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8792 (mt-10) REVERT: G 104 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: H 37 TYR cc_start: 0.9141 (m-80) cc_final: 0.8730 (m-80) REVERT: H 68 ASP cc_start: 0.9124 (t70) cc_final: 0.8818 (t0) REVERT: H 76 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8442 (mm-30) REVERT: H 79 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: K 89 LEU cc_start: 0.9243 (mt) cc_final: 0.8917 (tp) REVERT: L 42 SER cc_start: 0.7986 (m) cc_final: 0.7786 (p) REVERT: M 1 MET cc_start: 0.6272 (mtp) cc_final: 0.4807 (pmm) outliers start: 22 outliers final: 18 residues processed: 182 average time/residue: 0.1164 time to fit residues: 30.9515 Evaluate side-chains 185 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 12 optimal weight: 2.9990 chunk 86 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.060100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040192 restraints weight = 83869.691| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.38 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14582 Z= 0.145 Angle : 0.614 8.102 20973 Z= 0.361 Chirality : 0.041 0.310 2410 Planarity : 0.004 0.060 1663 Dihedral : 30.019 178.722 4261 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.35 % Allowed : 17.72 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.28), residues: 988 helix: 2.45 (0.21), residues: 647 sheet: -0.82 (0.99), residues: 28 loop : -0.58 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.017 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (14574) covalent geometry : angle 0.61226 / 0.36 (20964) hydrogen bonds : bond 0.08190 / 5.51 ( 823) hydrogen bonds : angle 3.15786 / 2.25 ( 2018) metal coordination : bond 0.00623 / 0.37 ( 8) metal coordination : angle 2.15882 / 1.76 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8560 (tt0) cc_final: 0.8279 (tt0) REVERT: C 64 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 95 LYS cc_start: 0.9121 (tptt) cc_final: 0.8729 (tppt) REVERT: D 63 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8595 (m-40) REVERT: D 68 ASP cc_start: 0.9036 (t70) cc_final: 0.8763 (t0) REVERT: E 94 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8335 (mt-10) REVERT: E 133 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 22 LEU cc_start: 0.8174 (pt) cc_final: 0.7897 (tt) REVERT: G 56 GLU cc_start: 0.8864 (tt0) cc_final: 0.8345 (tt0) REVERT: G 89 ASN cc_start: 0.9135 (m-40) cc_final: 0.8882 (m-40) REVERT: G 92 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8674 (mt-10) REVERT: H 37 TYR cc_start: 0.9135 (m-80) cc_final: 0.8743 (m-80) REVERT: H 68 ASP cc_start: 0.9110 (t70) cc_final: 0.8829 (t0) REVERT: H 76 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8420 (mm-30) REVERT: H 79 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8113 (mtm-85) REVERT: K 89 LEU cc_start: 0.9242 (mt) cc_final: 0.8904 (tp) REVERT: L 20 MET cc_start: 0.7307 (mmt) cc_final: 0.6841 (mpp) REVERT: L 42 SER cc_start: 0.7995 (m) cc_final: 0.7788 (p) REVERT: M 1 MET cc_start: 0.6265 (mtp) cc_final: 0.4972 (pmm) outliers start: 19 outliers final: 16 residues processed: 183 average time/residue: 0.1072 time to fit residues: 28.9360 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 75 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040068 restraints weight = 84961.540| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.39 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14582 Z= 0.156 Angle : 0.621 7.987 20973 Z= 0.364 Chirality : 0.041 0.306 2410 Planarity : 0.004 0.060 1663 Dihedral : 30.014 178.665 4259 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 17.47 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.28), residues: 988 helix: 2.40 (0.21), residues: 649 sheet: -0.78 (1.01), residues: 28 loop : -0.68 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.018 0.001 TYR F 88 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (14574) covalent geometry : angle 0.61956 / 0.36 (20964) hydrogen bonds : bond 0.08165 / 5.51 ( 823) hydrogen bonds : angle 3.18725 / 2.28 ( 2018) metal coordination : bond 0.00607 / 0.37 ( 8) metal coordination : angle 2.24811 / 1.87 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.54 seconds wall clock time: 42 minutes 54.54 seconds (2574.54 seconds total)