Starting phenix.real_space_refine on Fri Aug 7 13:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/08_2026/9ipu_60781.cif" } resolution = 4.3 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 8091 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 340 5.49 5 S 30 5.16 5 C 8838 2.51 5 N 2924 2.21 5 O 3616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 15750 Number of models: 1 Model: "" Number of chains: 15 Chain: "I" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 526 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" 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: "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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} 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: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "K" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1125 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 407 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 55} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3488 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "N" Number of atoms: 3484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3484 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} 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 7931 SG CYS L 31 64.159 100.830 26.967 1.00218.04 S ATOM 8073 SG CYS L 51 66.529 103.652 27.672 1.00210.14 S ATOM 8097 SG CYS L 54 63.002 104.560 26.813 1.00213.50 S ATOM 7822 SG CYS L 16 75.394 98.933 21.484 1.00283.03 S ATOM 7840 SG CYS L 19 78.982 98.250 20.552 1.00282.47 S ATOM 7970 SG CYS L 36 77.356 96.060 23.117 1.00253.66 S ATOM 7988 SG CYS L 39 78.088 99.560 24.108 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: 3.15, per 1000 atoms: 0.20 Number of scatterers: 15750 At special positions: 0 Unit cell: (124.584, 155.73, 110.622, 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 30 16.00 P 340 15.00 O 3616 8.00 N 2924 7.00 C 8838 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: 1.06 Conformation dependent library (CDL) restraints added in 508.5 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 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " Number of angles added : 9 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 62.1% alpha, 4.7% beta 148 base pairs and 314 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'I' and resid 27 through 39 Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 63 through 78 Processing helix chain 'A' and resid 44 through 55 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 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.815A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (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: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (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 124 removed outlier: 3.512A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.627A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 3.667A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.548A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.523A 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 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.515A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.587A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) 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 removed outlier: 3.549A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 2 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 10 through 15 Processing helix chain 'L' and resid 36 through 47 removed outlier: 4.833A pdb=" N GLU L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 69 removed outlier: 3.758A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 84 Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'I' and resid 45 through 46 removed outlier: 6.431A pdb=" N SER I 92 " --> pdb=" O THR I 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.469A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.816A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.062A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.292A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 38 Processing sheet with id=AB4, first strand: chain 'L' and resid 27 through 28 removed outlier: 3.552A pdb=" N LEU L 35 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 6 518 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 378 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 314 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3445 1.33 - 1.45: 5035 1.45 - 1.57: 7533 1.57 - 1.69: 677 1.69 - 1.81: 47 Bond restraints: 16737 Sorted by residual: bond pdb=" C1' DT N -78 " pdb=" N1 DT N -78 " ideal model delta sigma weight residual 1.468 1.569 -0.101 1.40e-02 5.10e+03 5.25e+01 bond pdb=" C3' DG N 79 " pdb=" O3' DG N 79 " ideal model delta sigma weight residual 1.435 1.341 0.094 1.30e-02 5.92e+03 5.18e+01 bond pdb=" C1' DT J -86 " pdb=" N1 DT J -86 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.08e+01 bond pdb=" C1' DT J -73 " pdb=" N1 DT J -73 " ideal model delta sigma weight residual 1.468 1.555 -0.087 1.40e-02 5.10e+03 3.88e+01 bond pdb=" C1' DT N 72 " pdb=" N1 DT N 72 " ideal model delta sigma weight residual 1.468 1.554 -0.086 1.40e-02 5.10e+03 3.74e+01 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 22377 2.29 - 4.57: 1553 4.57 - 6.86: 139 6.86 - 9.14: 35 9.14 - 11.43: 3 Bond angle restraints: 24107 Sorted by residual: angle pdb=" O4' DG J 21 " pdb=" C1' DG J 21 " pdb=" N9 DG J 21 " ideal model delta sigma weight residual 108.00 114.78 -6.78 7.00e-01 2.04e+00 9.39e+01 angle pdb=" C3' DT N 54 " pdb=" O3' DT N 54 " pdb=" P DC N 55 " ideal model delta sigma weight residual 119.70 129.30 -9.60 1.20e+00 6.94e-01 6.40e+01 angle pdb=" O5' DC J -23 " pdb=" C5' DC J -23 " pdb=" C4' DC J -23 " ideal model delta sigma weight residual 109.40 115.63 -6.23 8.00e-01 1.56e+00 6.06e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 119.70 128.82 -9.12 1.20e+00 6.94e-01 5.77e+01 angle pdb=" C3' DG J -58 " pdb=" O3' DG J -58 " pdb=" P DC J -57 " ideal model delta sigma weight residual 119.70 128.79 -9.09 1.20e+00 6.94e-01 5.74e+01 ... (remaining 24102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 7230 31.37 - 62.74: 1890 62.74 - 94.11: 52 94.11 - 125.48: 10 125.48 - 156.85: 3 Dihedral angle restraints: 9185 sinusoidal: 5901 harmonic: 3284 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 63.15 156.85 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT N 54 " pdb=" C3' DT N 54 " pdb=" O3' DT N 54 " pdb=" P DC N 55 " ideal model delta sinusoidal sigma weight residual 220.00 70.75 149.25 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 92.31 127.69 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2579 0.110 - 0.221: 161 0.221 - 0.331: 11 0.331 - 0.442: 1 0.442 - 0.552: 1 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C1' DC J 75 " pdb=" O4' DC J 75 " pdb=" C2' DC J 75 " pdb=" N1 DC J 75 " both_signs ideal model delta sigma weight residual False 2.43 1.88 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C3' DT N 54 " pdb=" C4' DT N 54 " pdb=" O3' DT N 54 " pdb=" C2' DT N 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1' DG N -76 " pdb=" O4' DG N -76 " pdb=" C2' DG N -76 " pdb=" N9 DG N -76 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2750 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 93 " 0.051 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE I 93 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 93 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE I 93 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE I 93 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 93 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 93 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N -77 " 0.045 2.00e-02 2.50e+03 2.43e-02 1.62e+01 pdb=" N9 DA N -77 " -0.062 2.00e-02 2.50e+03 pdb=" C8 DA N -77 " 0.018 2.00e-02 2.50e+03 pdb=" N7 DA N -77 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA N -77 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA N -77 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA N -77 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA N -77 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DA N -77 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA N -77 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA N -77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -76 " 0.027 2.00e-02 2.50e+03 1.69e-02 8.59e+00 pdb=" N9 DG N -76 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG N -76 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG N -76 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG N -76 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DG N -76 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG N -76 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG N -76 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG N -76 " 0.000 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 49 2.43 - 3.05: 9017 3.05 - 3.66: 25654 3.66 - 4.28: 40993 4.28 - 4.90: 60451 Nonbonded interactions: 136164 Sorted by model distance: nonbonded pdb=" NH1 ARG E 49 " pdb=" C5' DA N -66 " model vdw 1.810 3.520 nonbonded pdb=" CG2 THR A 45 " pdb=" OP1 DG N 70 " model vdw 1.933 3.460 nonbonded pdb=" NH1 ARG A 49 " pdb=" C5' DA J -66 " model vdw 2.017 3.520 nonbonded pdb=" NH1 ARG I 74 " pdb=" OP1 DC N 80 " model vdw 2.072 3.120 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG N 48 " model vdw 2.073 3.040 ... (remaining 136159 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'J' and (resid -82 through -1 or resid 1 through 83)) selection = (chain 'N' and (resid -82 through -1 or resid 1 through 83)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 16745 Z= 0.692 Angle : 1.197 11.426 24116 Z= 1.000 Chirality : 0.060 0.552 2753 Planarity : 0.005 0.092 1880 Dihedral : 27.547 156.849 7057 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.63 % Allowed : 4.35 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1100 helix: 1.86 (0.20), residues: 698 sheet: -0.65 (0.85), residues: 33 loop : -0.68 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 47 TYR 0.031 0.002 TYR I 28 PHE 0.051 0.002 PHE I 93 TRP 0.011 0.002 TRP K 93 HIS 0.009 0.001 HIS I 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.69 (16737) covalent geometry : angle 1.19614 / 1.00 (24107) hydrogen bonds : bond 0.16237 / 10.90 ( 896) hydrogen bonds : angle 6.08603 / 4.55 ( 2286) metal coordination : bond 0.00516 / 0.37 ( 8) metal coordination : angle 2.99243 / 2.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8250 (mt) cc_final: 0.7654 (mt) REVERT: A 106 ASP cc_start: 0.8636 (m-30) cc_final: 0.7922 (m-30) REVERT: E 120 MET cc_start: 0.7600 (ptp) cc_final: 0.7028 (ptm) REVERT: G 64 GLU cc_start: 0.9006 (tt0) cc_final: 0.8759 (tp30) REVERT: K 112 ASP cc_start: 0.9284 (t0) cc_final: 0.8934 (p0) REVERT: K 132 ASP cc_start: 0.9655 (t70) cc_final: 0.9432 (p0) REVERT: M 1 MET cc_start: 0.2658 (ptt) cc_final: 0.2381 (ptt) outliers start: 15 outliers final: 2 residues processed: 218 average time/residue: 0.1550 time to fit residues: 45.7478 Evaluate side-chains 90 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.040235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.028514 restraints weight = 236115.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.029114 restraints weight = 130554.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.029607 restraints weight = 89792.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029880 restraints weight = 69933.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.030094 restraints weight = 59425.295| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.004 0.078 16745 Z= 0.208 Angle : 0.914 13.336 24116 Z= 0.487 Chirality : 0.062 0.374 2753 Planarity : 0.006 0.067 1880 Dihedral : 31.521 155.314 4954 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.30 (0.26), residues: 1100 helix: 1.77 (0.19), residues: 697 sheet: -0.71 (0.83), residues: 33 loop : -0.72 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 29 TYR 0.014 0.002 TYR E 54 PHE 0.013 0.002 PHE A 67 TRP 0.013 0.003 TRP K 93 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.21 (16737) covalent geometry : angle 0.91209 / 0.49 (24107) hydrogen bonds : bond 0.07389 / 5.00 ( 896) hydrogen bonds : angle 3.78083 / 2.81 ( 2286) metal coordination : bond 0.00712 / 0.47 ( 8) metal coordination : angle 2.81627 / 1.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8513 (mtm-85) REVERT: A 90 MET cc_start: 0.9160 (mmp) cc_final: 0.8745 (mmp) REVERT: A 106 ASP cc_start: 0.9367 (m-30) cc_final: 0.8928 (m-30) REVERT: B 59 LYS cc_start: 0.9613 (tttp) cc_final: 0.9379 (tptp) REVERT: B 63 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9381 (pt0) REVERT: B 64 ASN cc_start: 0.9621 (m110) cc_final: 0.9233 (m110) REVERT: C 25 PHE cc_start: 0.9242 (m-10) cc_final: 0.8910 (m-10) REVERT: G 64 GLU cc_start: 0.9806 (tt0) cc_final: 0.9285 (tp30) REVERT: H 62 MET cc_start: 0.9612 (mmp) cc_final: 0.9263 (mmm) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.1469 time to fit residues: 26.5052 Evaluate side-chains 76 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 4 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 84 ASN K 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.038882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.027198 restraints weight = 241264.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.027841 restraints weight = 134086.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028221 restraints weight = 91868.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.028395 restraints weight = 71893.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.028504 restraints weight = 63169.430| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16745 Z= 0.190 Angle : 0.758 9.557 24116 Z= 0.419 Chirality : 0.052 0.358 2753 Planarity : 0.005 0.083 1880 Dihedral : 31.518 164.773 4954 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.29 (0.25), residues: 1100 helix: 1.76 (0.19), residues: 697 sheet: -1.19 (0.88), residues: 24 loop : -0.70 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K 139 TYR 0.018 0.002 TYR D 40 PHE 0.014 0.002 PHE A 104 TRP 0.011 0.002 TRP K 93 HIS 0.009 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (16737) covalent geometry : angle 0.75644 / 0.42 (24107) hydrogen bonds : bond 0.05997 / 4.08 ( 896) hydrogen bonds : angle 3.65517 / 2.74 ( 2286) metal coordination : bond 0.00569 / 0.34 ( 8) metal coordination : angle 2.33278 / 1.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9188 (mmp) cc_final: 0.8796 (mmp) REVERT: A 106 ASP cc_start: 0.9074 (m-30) cc_final: 0.8748 (m-30) REVERT: B 49 LEU cc_start: 0.9869 (mp) cc_final: 0.9443 (tt) REVERT: B 59 LYS cc_start: 0.9617 (tttp) cc_final: 0.9258 (tptp) REVERT: B 63 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9171 (mt-10) REVERT: B 64 ASN cc_start: 0.9663 (m110) cc_final: 0.9411 (m110) REVERT: D 59 MET cc_start: 0.9356 (tpt) cc_final: 0.9084 (tpt) REVERT: D 68 ASP cc_start: 0.9526 (t70) cc_final: 0.9313 (t0) REVERT: E 64 LYS cc_start: 0.9434 (mppt) cc_final: 0.9215 (mmtm) REVERT: G 64 GLU cc_start: 0.9796 (tt0) cc_final: 0.9507 (tm-30) REVERT: G 87 ILE cc_start: 0.9632 (mm) cc_final: 0.9369 (tp) REVERT: H 62 MET cc_start: 0.9617 (mmp) cc_final: 0.9268 (mmm) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1361 time to fit residues: 22.3645 Evaluate side-chains 73 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 0.1980 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 137 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 140 optimal weight: 50.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.037167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.025697 restraints weight = 246726.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.026237 restraints weight = 139441.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.026524 restraints weight = 96214.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026662 restraints weight = 77299.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026821 restraints weight = 69606.005| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16745 Z= 0.205 Angle : 0.748 8.777 24116 Z= 0.412 Chirality : 0.048 0.361 2753 Planarity : 0.005 0.040 1880 Dihedral : 31.622 179.706 4954 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.10 (0.25), residues: 1100 helix: 1.57 (0.19), residues: 697 sheet: -0.91 (0.88), residues: 24 loop : -0.70 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 139 TYR 0.025 0.002 TYR C 50 PHE 0.014 0.002 PHE E 67 TRP 0.019 0.002 TRP L 61 HIS 0.010 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.21 (16737) covalent geometry : angle 0.74663 / 0.41 (24107) hydrogen bonds : bond 0.07434 / 5.02 ( 896) hydrogen bonds : angle 3.66079 / 2.75 ( 2286) metal coordination : bond 0.00575 / 0.35 ( 8) metal coordination : angle 2.30287 / 1.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9207 (mmp) cc_final: 0.8862 (mmp) REVERT: B 49 LEU cc_start: 0.9857 (mp) cc_final: 0.9572 (tt) REVERT: B 64 ASN cc_start: 0.9680 (m110) cc_final: 0.9403 (m110) REVERT: D 59 MET cc_start: 0.9049 (tpp) cc_final: 0.8709 (tpp) REVERT: D 68 ASP cc_start: 0.9512 (t70) cc_final: 0.9300 (t0) REVERT: E 64 LYS cc_start: 0.9531 (mppt) cc_final: 0.9318 (mmtm) REVERT: G 64 GLU cc_start: 0.9786 (tt0) cc_final: 0.9485 (tm-30) REVERT: G 87 ILE cc_start: 0.9641 (mm) cc_final: 0.9369 (tp) REVERT: H 62 MET cc_start: 0.9641 (mmp) cc_final: 0.9316 (mmp) REVERT: K 38 MET cc_start: 0.9510 (mmp) cc_final: 0.9275 (tpt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1319 time to fit residues: 19.3130 Evaluate side-chains 71 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.037707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.026192 restraints weight = 243088.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.026774 restraints weight = 137401.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.027071 restraints weight = 94871.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.027280 restraints weight = 76856.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.027351 restraints weight = 67659.112| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (20 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16745 Z= 0.144 Angle : 0.664 8.646 24116 Z= 0.373 Chirality : 0.046 0.321 2753 Planarity : 0.005 0.052 1880 Dihedral : 31.442 179.590 4954 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.28 (0.25), residues: 1100 helix: 1.75 (0.19), residues: 699 sheet: -1.43 (0.84), residues: 24 loop : -0.70 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 49 TYR 0.020 0.001 TYR L 64 PHE 0.009 0.001 PHE F 61 TRP 0.008 0.001 TRP L 61 HIS 0.013 0.001 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (16737) covalent geometry : angle 0.66298 / 0.37 (24107) hydrogen bonds : bond 0.04249 / 2.87 ( 896) hydrogen bonds : angle 3.48651 / 2.63 ( 2286) metal coordination : bond 0.00436 / 0.25 ( 8) metal coordination : angle 1.87968 / 1.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9215 (mmp) cc_final: 0.8919 (mmp) REVERT: B 49 LEU cc_start: 0.9866 (mp) cc_final: 0.9577 (tt) REVERT: B 64 ASN cc_start: 0.9661 (m110) cc_final: 0.9393 (m110) REVERT: D 68 ASP cc_start: 0.9509 (t70) cc_final: 0.9289 (t0) REVERT: D 102 LEU cc_start: 0.9520 (mm) cc_final: 0.9027 (tp) REVERT: E 64 LYS cc_start: 0.9546 (mppt) cc_final: 0.9327 (mmtm) REVERT: E 106 ASP cc_start: 0.9248 (m-30) cc_final: 0.9045 (m-30) REVERT: G 64 GLU cc_start: 0.9802 (tt0) cc_final: 0.9480 (tm-30) REVERT: G 87 ILE cc_start: 0.9633 (mm) cc_final: 0.9335 (tp) REVERT: H 59 MET cc_start: 0.9556 (tpt) cc_final: 0.9339 (tpt) REVERT: H 62 MET cc_start: 0.9631 (mmp) cc_final: 0.9251 (mmp) REVERT: K 38 MET cc_start: 0.9584 (mmp) cc_final: 0.9060 (tpt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1352 time to fit residues: 20.3204 Evaluate side-chains 70 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 8.9990 chunk 118 optimal weight: 40.0000 chunk 36 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 133 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS K 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.036016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.025269 restraints weight = 253690.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025701 restraints weight = 152728.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025641 restraints weight = 105573.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.025774 restraints weight = 85386.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025955 restraints weight = 74759.883| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16745 Z= 0.207 Angle : 0.704 7.596 24116 Z= 0.393 Chirality : 0.045 0.277 2753 Planarity : 0.005 0.052 1880 Dihedral : 31.454 178.384 4954 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.19 (0.25), residues: 1100 helix: 1.67 (0.19), residues: 700 sheet: -1.79 (0.90), residues: 24 loop : -0.67 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 129 TYR 0.015 0.002 TYR E 54 PHE 0.011 0.002 PHE E 67 TRP 0.008 0.001 TRP K 93 HIS 0.007 0.001 HIS L 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.21 (16737) covalent geometry : angle 0.70283 / 0.39 (24107) hydrogen bonds : bond 0.08565 / 5.74 ( 896) hydrogen bonds : angle 3.66500 / 2.74 ( 2286) metal coordination : bond 0.00679 / 0.39 ( 8) metal coordination : angle 1.77606 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9234 (mmp) cc_final: 0.8941 (mmp) REVERT: A 120 MET cc_start: 0.8784 (mtm) cc_final: 0.8333 (mtt) REVERT: B 59 LYS cc_start: 0.9676 (tttp) cc_final: 0.9372 (tptm) REVERT: B 63 GLU cc_start: 0.9738 (pt0) cc_final: 0.9514 (pt0) REVERT: C 25 PHE cc_start: 0.9395 (m-80) cc_final: 0.9128 (m-10) REVERT: D 59 MET cc_start: 0.9179 (tpp) cc_final: 0.8887 (tpp) REVERT: D 102 LEU cc_start: 0.9541 (mm) cc_final: 0.9160 (tp) REVERT: E 64 LYS cc_start: 0.9589 (mppt) cc_final: 0.9363 (mmtm) REVERT: G 87 ILE cc_start: 0.9638 (mm) cc_final: 0.9358 (tp) REVERT: H 62 MET cc_start: 0.9666 (mmp) cc_final: 0.9315 (mmp) REVERT: K 38 MET cc_start: 0.9525 (mmp) cc_final: 0.8857 (tpt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1389 time to fit residues: 19.6647 Evaluate side-chains 66 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 136 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 6 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 GLN ** 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 = 0.3107 r_free = 0.3107 target = 0.036325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.024976 restraints weight = 247238.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.025418 restraints weight = 139963.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.025597 restraints weight = 99444.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025938 restraints weight = 87121.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026133 restraints weight = 74989.435| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16745 Z= 0.161 Angle : 0.655 7.562 24116 Z= 0.370 Chirality : 0.044 0.252 2753 Planarity : 0.005 0.059 1880 Dihedral : 31.444 178.316 4954 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.22 (0.25), residues: 1100 helix: 1.71 (0.19), residues: 702 sheet: -1.55 (0.86), residues: 24 loop : -0.73 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 134 TYR 0.026 0.002 TYR L 64 PHE 0.009 0.001 PHE F 61 TRP 0.007 0.001 TRP K 93 HIS 0.018 0.001 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (16737) covalent geometry : angle 0.65387 / 0.37 (24107) hydrogen bonds : bond 0.04951 / 3.33 ( 896) hydrogen bonds : angle 3.59630 / 2.68 ( 2286) metal coordination : bond 0.00504 / 0.28 ( 8) metal coordination : angle 1.76201 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9236 (mmp) cc_final: 0.8928 (mmp) REVERT: A 120 MET cc_start: 0.8736 (mtm) cc_final: 0.8332 (mtp) REVERT: B 49 LEU cc_start: 0.9869 (mp) cc_final: 0.9356 (tt) REVERT: B 59 LYS cc_start: 0.9682 (tttp) cc_final: 0.9340 (tptm) REVERT: B 63 GLU cc_start: 0.9718 (pt0) cc_final: 0.9426 (pt0) REVERT: C 25 PHE cc_start: 0.9413 (m-80) cc_final: 0.9178 (m-80) REVERT: D 102 LEU cc_start: 0.9541 (mm) cc_final: 0.9223 (tp) REVERT: E 64 LYS cc_start: 0.9590 (mppt) cc_final: 0.9366 (mmtm) REVERT: G 87 ILE cc_start: 0.9625 (mm) cc_final: 0.9341 (tp) REVERT: G 104 GLN cc_start: 0.9476 (mm-40) cc_final: 0.9128 (mm-40) REVERT: H 59 MET cc_start: 0.9591 (tpt) cc_final: 0.9370 (tpt) REVERT: H 62 MET cc_start: 0.9620 (mmp) cc_final: 0.9286 (mmp) REVERT: K 38 MET cc_start: 0.9593 (mmp) cc_final: 0.9103 (tpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1322 time to fit residues: 18.6833 Evaluate side-chains 67 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 80 optimal weight: 0.3980 chunk 92 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.0040 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 GLN ** 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 = 0.3108 r_free = 0.3108 target = 0.036442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024911 restraints weight = 254893.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.025364 restraints weight = 145193.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025789 restraints weight = 105586.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026039 restraints weight = 86288.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.026064 restraints weight = 73945.192| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16745 Z= 0.145 Angle : 0.645 7.309 24116 Z= 0.364 Chirality : 0.043 0.258 2753 Planarity : 0.004 0.057 1880 Dihedral : 31.202 178.421 4954 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.24 (0.25), residues: 1100 helix: 1.70 (0.19), residues: 709 sheet: -1.39 (0.88), residues: 24 loop : -0.75 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.009 0.001 TYR C 57 PHE 0.012 0.001 PHE A 104 TRP 0.007 0.001 TRP L 61 HIS 0.005 0.001 HIS L 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (16737) covalent geometry : angle 0.64418 / 0.36 (24107) hydrogen bonds : bond 0.04532 / 3.06 ( 896) hydrogen bonds : angle 3.53051 / 2.62 ( 2286) metal coordination : bond 0.00416 / 0.22 ( 8) metal coordination : angle 1.48207 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9226 (mmp) cc_final: 0.8927 (mmp) REVERT: A 120 MET cc_start: 0.8688 (mtm) cc_final: 0.8259 (mtp) REVERT: B 49 LEU cc_start: 0.9866 (mp) cc_final: 0.9337 (tt) REVERT: B 59 LYS cc_start: 0.9672 (tttp) cc_final: 0.9307 (tptm) REVERT: B 63 GLU cc_start: 0.9727 (pt0) cc_final: 0.9343 (pt0) REVERT: C 25 PHE cc_start: 0.9398 (m-80) cc_final: 0.8993 (m-10) REVERT: C 95 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8862 (pttm) REVERT: D 59 MET cc_start: 0.9413 (tpt) cc_final: 0.9120 (tpt) REVERT: D 102 LEU cc_start: 0.9523 (mm) cc_final: 0.9200 (tp) REVERT: E 64 LYS cc_start: 0.9613 (mppt) cc_final: 0.9383 (mmtm) REVERT: G 87 ILE cc_start: 0.9611 (mm) cc_final: 0.9312 (tp) REVERT: G 104 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9119 (mm-40) REVERT: H 59 MET cc_start: 0.9558 (tpt) cc_final: 0.9356 (tpt) REVERT: H 62 MET cc_start: 0.9612 (mmp) cc_final: 0.9283 (mmp) REVERT: K 38 MET cc_start: 0.9588 (mmp) cc_final: 0.9137 (tpp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1390 time to fit residues: 20.4617 Evaluate side-chains 68 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 7.9990 chunk 120 optimal weight: 40.0000 chunk 129 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 118 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.035420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024220 restraints weight = 254512.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024657 restraints weight = 150904.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025082 restraints weight = 108316.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025194 restraints weight = 86675.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025196 restraints weight = 76988.039| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16745 Z= 0.200 Angle : 0.676 7.371 24116 Z= 0.380 Chirality : 0.043 0.249 2753 Planarity : 0.005 0.060 1880 Dihedral : 31.298 177.754 4954 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.19 (0.25), residues: 1100 helix: 1.62 (0.19), residues: 707 sheet: -1.06 (0.95), residues: 22 loop : -0.69 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 99 TYR 0.015 0.002 TYR D 40 PHE 0.011 0.001 PHE D 65 TRP 0.007 0.001 TRP L 61 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 (16737) covalent geometry : angle 0.67541 / 0.38 (24107) hydrogen bonds : bond 0.07021 / 4.69 ( 896) hydrogen bonds : angle 3.69205 / 2.74 ( 2286) metal coordination : bond 0.00692 / 0.39 ( 8) metal coordination : angle 1.63364 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9243 (mmp) cc_final: 0.8960 (mmp) REVERT: A 99 TYR cc_start: 0.9429 (t80) cc_final: 0.9214 (t80) REVERT: A 120 MET cc_start: 0.8589 (mtm) cc_final: 0.8104 (mtp) REVERT: B 59 LYS cc_start: 0.9689 (tttp) cc_final: 0.9326 (tptm) REVERT: B 63 GLU cc_start: 0.9740 (pt0) cc_final: 0.9367 (pt0) REVERT: D 59 MET cc_start: 0.9253 (tpp) cc_final: 0.8960 (tpt) REVERT: D 71 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9065 (mt-10) REVERT: D 102 LEU cc_start: 0.9536 (mm) cc_final: 0.9206 (tp) REVERT: E 64 LYS cc_start: 0.9625 (mppt) cc_final: 0.9415 (mmtm) REVERT: G 64 GLU cc_start: 0.9803 (tt0) cc_final: 0.9464 (tm-30) REVERT: G 87 ILE cc_start: 0.9611 (mm) cc_final: 0.9302 (tp) REVERT: G 104 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9185 (mm-40) REVERT: H 62 MET cc_start: 0.9634 (mmp) cc_final: 0.9312 (mmp) REVERT: K 38 MET cc_start: 0.9564 (mmp) cc_final: 0.9053 (tpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1414 time to fit residues: 19.0215 Evaluate side-chains 64 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 121 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.035980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024553 restraints weight = 255284.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.025016 restraints weight = 145678.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.025427 restraints weight = 106112.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025475 restraints weight = 87326.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025475 restraints weight = 79572.965| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16745 Z= 0.145 Angle : 0.635 7.359 24116 Z= 0.360 Chirality : 0.043 0.256 2753 Planarity : 0.004 0.060 1880 Dihedral : 31.190 177.475 4954 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.31 (0.25), residues: 1100 helix: 1.75 (0.19), residues: 708 sheet: -0.90 (0.98), residues: 22 loop : -0.73 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 129 TYR 0.017 0.001 TYR L 64 PHE 0.009 0.001 PHE A 104 TRP 0.005 0.001 TRP L 61 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (16737) covalent geometry : angle 0.63420 / 0.36 (24107) hydrogen bonds : bond 0.04117 / 2.80 ( 896) hydrogen bonds : angle 3.56129 / 2.66 ( 2286) metal coordination : bond 0.00457 / 0.24 ( 8) metal coordination : angle 1.58232 / 1.22 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9356 (t80) cc_final: 0.8992 (t80) REVERT: C 25 PHE cc_start: 0.9299 (m-80) cc_final: 0.8753 (m-80) REVERT: C 79 ILE cc_start: 0.9648 (tp) cc_final: 0.9440 (pt) REVERT: D 102 LEU cc_start: 0.9084 (mm) cc_final: 0.8743 (tp) REVERT: G 87 ILE cc_start: 0.9112 (mm) cc_final: 0.8820 (tp) REVERT: H 62 MET cc_start: 0.9866 (mmp) cc_final: 0.9653 (mmm) REVERT: K 38 MET cc_start: 0.9448 (mmp) cc_final: 0.9087 (tpp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1373 time to fit residues: 18.9567 Evaluate side-chains 64 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.035908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024707 restraints weight = 255961.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025155 restraints weight = 149447.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.025333 restraints weight = 107487.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025453 restraints weight = 87976.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025453 restraints weight = 78660.508| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16745 Z= 0.145 Angle : 0.635 7.228 24116 Z= 0.360 Chirality : 0.042 0.263 2753 Planarity : 0.004 0.060 1880 Dihedral : 31.070 178.182 4954 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % 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: 1.34 (0.25), residues: 1100 helix: 1.77 (0.19), residues: 708 sheet: -0.68 (1.03), residues: 22 loop : -0.71 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 99 TYR 0.013 0.001 TYR D 40 PHE 0.008 0.001 PHE F 61 TRP 0.005 0.001 TRP L 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (16737) covalent geometry : angle 0.63404 / 0.36 (24107) hydrogen bonds : bond 0.04785 / 3.23 ( 896) hydrogen bonds : angle 3.53615 / 2.64 ( 2286) metal coordination : bond 0.00484 / 0.26 ( 8) metal coordination : angle 1.46687 / 1.05 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.31 seconds wall clock time: 43 minutes 15.28 seconds (2595.28 seconds total)