Starting phenix.real_space_refine on Sat Jul 4 16:09:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/07_2026/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/07_2026/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/07_2026/9ipu_60781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ipu_60781/07_2026/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/07_2026/9ipu_60781.map" } 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-dev-6108/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: 2.94, per 1000 atoms: 0.19 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: 1.30 Conformation dependent library (CDL) restraints added in 416.3 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: 2.28 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: 2.96 Time building geometry restraints manager: 1.74 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: 22421 2.29 - 4.57: 1520 4.57 - 6.86: 131 6.86 - 9.14: 33 9.14 - 11.43: 2 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=" 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=" O4' DG N -2 " pdb=" C1' DG N -2 " pdb=" N9 DG N -2 " ideal model delta sigma weight residual 108.00 113.18 -5.18 7.00e-01 2.04e+00 5.47e+01 angle pdb=" O4' DC J 75 " pdb=" C1' DC J 75 " pdb=" N1 DC J 75 " ideal model delta sigma weight residual 108.00 113.13 -5.13 7.00e-01 2.04e+00 5.36e+01 angle pdb=" O4' DC N -10 " pdb=" C1' DC N -10 " pdb=" N1 DC N -10 " ideal model delta sigma weight residual 108.00 113.11 -5.11 7.00e-01 2.04e+00 5.34e+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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- 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= 0.690 Angle : 1.181 11.426 24116 Z= 0.974 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 1.17976 / 0.97 (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 : 0.409 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: 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: 0.7923 (m-30) REVERT: E 120 MET cc_start: 0.7600 (ptp) cc_final: 0.7032 (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: 0.2386 (ptt) outliers start: 15 outliers final: 2 residues processed: 218 average time/residue: 0.1620 time to fit residues: 47.5092 Evaluate side-chains 93 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 30.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 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 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 = 0.3245 r_free = 0.3245 target = 0.040292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028561 restraints weight = 236826.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029208 restraints weight = 128585.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.029612 restraints weight = 87028.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029802 restraints weight = 68619.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029885 restraints weight = 60463.461| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16745 Z= 0.200 Angle : 0.907 13.164 24116 Z= 0.486 Chirality : 0.061 0.379 2753 Planarity : 0.006 0.058 1880 Dihedral : 31.628 154.996 4954 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 1.25 (0.25), residues: 1100 helix: 1.71 (0.19), residues: 697 sheet: -1.11 (0.95), residues: 24 loop : -0.69 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.014 0.002 TYR E 54 PHE 0.014 0.002 PHE A 67 TRP 0.028 0.004 TRP K 33 HIS 0.008 0.001 HIS L 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 (16737) covalent geometry : angle 0.90575 / 0.49 (24107) hydrogen bonds : bond 0.07362 / 4.98 ( 896) hydrogen bonds : angle 3.80315 / 2.82 ( 2286) metal coordination : bond 0.00805 / 0.51 ( 8) metal coordination : angle 2.93248 / 2.02 ( 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 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9167 (mmp) cc_final: 0.8757 (mmp) REVERT: A 106 ASP cc_start: 0.9361 (m-30) cc_final: 0.8889 (m-30) REVERT: B 59 LYS cc_start: 0.9616 (tttp) cc_final: 0.9385 (tptp) REVERT: B 63 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9378 (pt0) REVERT: B 64 ASN cc_start: 0.9621 (m110) cc_final: 0.9230 (m110) REVERT: C 25 PHE cc_start: 0.9245 (m-10) cc_final: 0.8926 (m-10) REVERT: E 106 ASP cc_start: 0.9380 (m-30) cc_final: 0.8717 (m-30) REVERT: E 120 MET cc_start: 0.9040 (ptp) cc_final: 0.8796 (ptp) REVERT: F 44 LYS cc_start: 0.9237 (tptp) cc_final: 0.8978 (tptp) REVERT: G 64 GLU cc_start: 0.9812 (tt0) cc_final: 0.9298 (tp30) REVERT: H 62 MET cc_start: 0.9628 (mmp) cc_final: 0.9277 (mmm) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.1447 time to fit residues: 25.8713 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 : 0.438 ------------------------------------------------------------------------------- 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: 20.0000 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 0.0170 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 chunk 82 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.0424 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.040098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.028296 restraints weight = 236550.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028952 restraints weight = 128519.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.029298 restraints weight = 86553.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029582 restraints weight = 68469.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.029650 restraints weight = 59138.985| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16745 Z= 0.158 Angle : 0.721 8.949 24116 Z= 0.405 Chirality : 0.051 0.358 2753 Planarity : 0.004 0.050 1880 Dihedral : 31.482 162.994 4954 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.22 % Allowed : 3.05 % Favored : 96.74 % 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: 1.76 (0.20), residues: 699 sheet: -1.13 (0.87), residues: 24 loop : -0.68 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 139 TYR 0.016 0.002 TYR D 40 PHE 0.013 0.001 PHE A 104 TRP 0.011 0.002 TRP L 61 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (16737) covalent geometry : angle 0.71982 / 0.41 (24107) hydrogen bonds : bond 0.04799 / 3.26 ( 896) hydrogen bonds : angle 3.52885 / 2.66 ( 2286) metal coordination : bond 0.00436 / 0.27 ( 8) metal coordination : angle 2.23756 / 1.74 ( 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 125 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9203 (mmp) cc_final: 0.8806 (mmp) REVERT: A 106 ASP cc_start: 0.9101 (m-30) cc_final: 0.8770 (m-30) REVERT: B 49 LEU cc_start: 0.9871 (mp) cc_final: 0.9470 (tt) REVERT: B 59 LYS cc_start: 0.9608 (tttp) cc_final: 0.9292 (tptp) REVERT: B 63 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9181 (mt-10) REVERT: B 64 ASN cc_start: 0.9656 (m110) cc_final: 0.9392 (m110) REVERT: D 59 MET cc_start: 0.9384 (tpt) cc_final: 0.9116 (tpt) REVERT: D 68 ASP cc_start: 0.9532 (t70) cc_final: 0.9304 (t0) REVERT: E 106 ASP cc_start: 0.9240 (m-30) cc_final: 0.8819 (m-30) REVERT: E 120 MET cc_start: 0.8878 (ptp) cc_final: 0.8517 (ptp) REVERT: G 64 GLU cc_start: 0.9801 (tt0) cc_final: 0.9264 (tp30) REVERT: G 87 ILE cc_start: 0.9610 (mm) cc_final: 0.9331 (tp) REVERT: H 59 MET cc_start: 0.9565 (tpt) cc_final: 0.9332 (tpt) REVERT: H 62 MET cc_start: 0.9606 (mmp) cc_final: 0.9253 (mmm) REVERT: H 101 LEU cc_start: 0.9225 (mm) cc_final: 0.8940 (mt) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1601 time to fit residues: 27.6741 Evaluate side-chains 79 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 140 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN D 109 HIS G 112 GLN K 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.036449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.024964 restraints weight = 251857.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.025471 restraints weight = 144356.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.025734 restraints weight = 101128.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.025918 restraints weight = 81482.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.025974 restraints weight = 73128.720| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 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 = 0.2792 r_free = 0.2792 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 (9 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16745 Z= 0.271 Angle : 0.801 11.376 24116 Z= 0.443 Chirality : 0.050 0.332 2753 Planarity : 0.005 0.046 1880 Dihedral : 31.858 177.759 4954 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.06 (0.25), residues: 1100 helix: 1.44 (0.19), residues: 694 sheet: -1.04 (0.93), residues: 24 loop : -0.48 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 139 TYR 0.032 0.003 TYR L 64 PHE 0.018 0.002 PHE E 67 TRP 0.021 0.003 TRP L 61 HIS 0.011 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.27 (16737) covalent geometry : angle 0.79982 / 0.44 (24107) hydrogen bonds : bond 0.11904 / 8.00 ( 896) hydrogen bonds : angle 3.84633 / 2.87 ( 2286) metal coordination : bond 0.00764 / 0.47 ( 8) metal coordination : angle 2.41800 / 1.74 ( 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 95 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.446 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: 0.9230 (mmp) cc_final: 0.8846 (mmp) REVERT: B 49 LEU cc_start: 0.9842 (mp) cc_final: 0.9516 (tt) REVERT: B 64 ASN cc_start: 0.9711 (m110) cc_final: 0.9450 (m110) REVERT: C 25 PHE cc_start: 0.9330 (m-10) cc_final: 0.8833 (m-10) REVERT: D 68 ASP cc_start: 0.9479 (t70) cc_final: 0.9270 (t0) REVERT: E 64 LYS cc_start: 0.9533 (mppt) cc_final: 0.9332 (mmtm) REVERT: E 120 MET cc_start: 0.8458 (ptp) cc_final: 0.8084 (ptp) REVERT: F 84 MET cc_start: 0.9423 (mmm) cc_final: 0.9207 (mmm) REVERT: G 87 ILE cc_start: 0.9647 (mm) cc_final: 0.9385 (tp) REVERT: H 62 MET cc_start: 0.9649 (mmp) cc_final: 0.9341 (mmp) REVERT: K 38 MET cc_start: 0.9578 (mmp) cc_final: 0.9027 (tpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1601 time to fit residues: 21.3345 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 : 0.470 ------------------------------------------------------------------------------- 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: 20.0000 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.037038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.025526 restraints weight = 245514.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026046 restraints weight = 140482.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.026233 restraints weight = 99887.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026462 restraints weight = 85000.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.026704 restraints weight = 75279.658| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 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 = 0.2806 r_free = 0.2806 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 (11 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16745 Z= 0.168 Angle : 0.663 7.978 24116 Z= 0.376 Chirality : 0.046 0.285 2753 Planarity : 0.005 0.052 1880 Dihedral : 31.832 179.551 4954 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.21 (0.25), residues: 1100 helix: 1.66 (0.19), residues: 699 sheet: -1.09 (0.86), residues: 24 loop : -0.65 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 23 TYR 0.015 0.001 TYR L 64 PHE 0.010 0.001 PHE F 61 TRP 0.008 0.001 TRP L 61 HIS 0.017 0.002 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (16737) covalent geometry : angle 0.66095 / 0.38 (24107) hydrogen bonds : bond 0.04700 / 3.15 ( 896) hydrogen bonds : angle 3.60827 / 2.71 ( 2286) metal coordination : bond 0.00533 / 0.31 ( 8) metal coordination : angle 2.52928 / 2.09 ( 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 99 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.473 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: 0.9214 (mmp) cc_final: 0.8898 (mmp) REVERT: A 120 MET cc_start: 0.8628 (mtm) cc_final: 0.8342 (mtt) REVERT: B 49 LEU cc_start: 0.9863 (mp) cc_final: 0.9414 (tt) REVERT: B 64 ASN cc_start: 0.9669 (m110) cc_final: 0.9426 (m110) REVERT: D 68 ASP cc_start: 0.9520 (t70) cc_final: 0.9293 (t0) REVERT: G 64 GLU cc_start: 0.9791 (tt0) cc_final: 0.9475 (tm-30) REVERT: G 87 ILE cc_start: 0.9651 (mm) cc_final: 0.9376 (tp) REVERT: H 62 MET cc_start: 0.9629 (mmp) cc_final: 0.9259 (mmp) REVERT: H 72 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8750 (mtp85) REVERT: K 38 MET cc_start: 0.9440 (mmp) cc_final: 0.8929 (tpp) REVERT: K 147 MET cc_start: 0.8306 (mmp) cc_final: 0.7727 (mpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1587 time to fit residues: 22.0160 Evaluate side-chains 65 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 133 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.035347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.024066 restraints weight = 257364.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024446 restraints weight = 148841.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.024817 restraints weight = 108048.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.024866 restraints weight = 90197.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025124 restraints weight = 82649.174| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 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 = 0.2754 r_free = 0.2754 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 (6 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16745 Z= 0.241 Angle : 0.725 8.480 24116 Z= 0.406 Chirality : 0.046 0.253 2753 Planarity : 0.005 0.053 1880 Dihedral : 31.819 178.073 4954 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.11 % Allowed : 2.07 % Favored : 97.82 % 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: 1.00 (0.25), residues: 1100 helix: 1.44 (0.19), residues: 705 sheet: -1.01 (0.85), residues: 24 loop : -0.66 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 128 TYR 0.017 0.002 TYR E 54 PHE 0.014 0.002 PHE A 104 TRP 0.010 0.002 TRP K 93 HIS 0.012 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.24 (16737) covalent geometry : angle 0.72398 / 0.41 (24107) hydrogen bonds : bond 0.09906 / 6.62 ( 896) hydrogen bonds : angle 3.88054 / 2.90 ( 2286) metal coordination : bond 0.00796 / 0.46 ( 8) metal coordination : angle 2.28904 / 1.73 ( 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 93 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9265 (mmp) cc_final: 0.8963 (mmp) REVERT: B 49 LEU cc_start: 0.9867 (mp) cc_final: 0.9569 (tt) REVERT: B 64 ASN cc_start: 0.9707 (m110) cc_final: 0.9462 (m110) REVERT: C 25 PHE cc_start: 0.9374 (m-80) cc_final: 0.8924 (m-10) REVERT: D 59 MET cc_start: 0.9440 (tpt) cc_final: 0.9092 (tpt) REVERT: E 64 LYS cc_start: 0.9573 (mppt) cc_final: 0.9350 (mmtm) REVERT: E 106 ASP cc_start: 0.9297 (m-30) cc_final: 0.9056 (m-30) REVERT: E 120 MET cc_start: 0.8729 (ptp) cc_final: 0.8240 (ptp) REVERT: G 64 GLU cc_start: 0.9803 (tt0) cc_final: 0.9460 (tm-30) REVERT: G 87 ILE cc_start: 0.9655 (mm) cc_final: 0.9368 (tp) REVERT: H 62 MET cc_start: 0.9648 (mmp) cc_final: 0.9316 (mmp) REVERT: H 72 ARG cc_start: 0.9210 (mtt180) cc_final: 0.8923 (mtp85) REVERT: K 38 MET cc_start: 0.9457 (mmp) cc_final: 0.8888 (tpp) REVERT: K 147 MET cc_start: 0.8299 (mmp) cc_final: 0.7755 (mpp) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1414 time to fit residues: 18.3926 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 : 0.494 ------------------------------------------------------------------------------- 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: 6.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 136 optimal weight: 40.0000 chunk 96 optimal weight: 40.0000 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 128 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.036198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.024824 restraints weight = 253694.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.025290 restraints weight = 146018.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.025571 restraints weight = 103077.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.025804 restraints weight = 84211.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.025813 restraints weight = 74542.213| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 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 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16745 Z= 0.153 Angle : 0.645 7.190 24116 Z= 0.368 Chirality : 0.045 0.238 2753 Planarity : 0.005 0.060 1880 Dihedral : 31.762 178.178 4954 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 1.12 (0.25), residues: 1100 helix: 1.53 (0.19), residues: 706 sheet: -0.79 (0.84), residues: 24 loop : -0.65 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 128 TYR 0.020 0.001 TYR L 64 PHE 0.009 0.001 PHE F 61 TRP 0.008 0.001 TRP K 93 HIS 0.017 0.001 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (16737) covalent geometry : angle 0.64431 / 0.37 (24107) hydrogen bonds : bond 0.04722 / 3.17 ( 896) hydrogen bonds : angle 3.68907 / 2.76 ( 2286) metal coordination : bond 0.00462 / 0.25 ( 8) metal coordination : angle 2.11687 / 1.55 ( 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 92 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.489 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: 0.9243 (mmp) cc_final: 0.8941 (mmp) REVERT: B 49 LEU cc_start: 0.9866 (mp) cc_final: 0.9550 (tt) REVERT: B 64 ASN cc_start: 0.9704 (m110) cc_final: 0.9480 (m110) REVERT: D 102 LEU cc_start: 0.9531 (mm) cc_final: 0.9215 (tp) REVERT: E 120 MET cc_start: 0.8416 (ptp) cc_final: 0.8064 (ptp) REVERT: G 64 GLU cc_start: 0.9803 (tt0) cc_final: 0.9462 (tm-30) REVERT: G 87 ILE cc_start: 0.9627 (mm) cc_final: 0.9325 (tp) REVERT: G 104 GLN cc_start: 0.9476 (mm-40) cc_final: 0.9155 (mm-40) REVERT: H 59 MET cc_start: 0.9580 (tpt) cc_final: 0.9348 (tpt) REVERT: H 62 MET cc_start: 0.9632 (mmp) cc_final: 0.9295 (mmp) REVERT: H 72 ARG cc_start: 0.9186 (mtt180) cc_final: 0.8888 (mtp85) REVERT: K 38 MET cc_start: 0.9436 (mmp) cc_final: 0.8813 (tpp) REVERT: K 147 MET cc_start: 0.8224 (mmp) cc_final: 0.7676 (mtt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1539 time to fit residues: 19.7743 Evaluate side-chains 61 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 20.0000 chunk 121 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 46 GLN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.024063 restraints weight = 259637.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024581 restraints weight = 149601.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.024724 restraints weight = 106669.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.025037 restraints weight = 92561.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025112 restraints weight = 80620.692| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 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: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16745 Z= 0.181 Angle : 0.658 8.631 24116 Z= 0.375 Chirality : 0.043 0.235 2753 Planarity : 0.005 0.058 1880 Dihedral : 31.610 177.796 4954 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.09 (0.25), residues: 1100 helix: 1.52 (0.19), residues: 704 sheet: -0.70 (0.83), residues: 24 loop : -0.66 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 32 TYR 0.012 0.002 TYR E 54 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP K 93 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (16737) covalent geometry : angle 0.65676 / 0.38 (24107) hydrogen bonds : bond 0.06435 / 4.32 ( 896) hydrogen bonds : angle 3.76478 / 2.81 ( 2286) metal coordination : bond 0.00600 / 0.33 ( 8) metal coordination : angle 2.07941 / 1.47 ( 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 90 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.338 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: 0.9211 (mmp) cc_final: 0.8940 (mmp) REVERT: B 64 ASN cc_start: 0.9711 (m110) cc_final: 0.9508 (m110) REVERT: C 25 PHE cc_start: 0.9380 (m-80) cc_final: 0.9092 (m-10) REVERT: D 102 LEU cc_start: 0.9527 (mm) cc_final: 0.9183 (tp) REVERT: E 120 MET cc_start: 0.8394 (ptp) cc_final: 0.8045 (ptp) REVERT: G 36 LYS cc_start: 0.9618 (ptpp) cc_final: 0.9404 (pttm) REVERT: G 64 GLU cc_start: 0.9802 (tt0) cc_final: 0.9438 (tm-30) REVERT: G 87 ILE cc_start: 0.9624 (mm) cc_final: 0.9315 (tp) REVERT: G 104 GLN cc_start: 0.9475 (mm-40) cc_final: 0.9162 (mm-40) REVERT: H 62 MET cc_start: 0.9637 (mmp) cc_final: 0.9301 (mmp) REVERT: K 38 MET cc_start: 0.9457 (mmp) cc_final: 0.8890 (tpp) REVERT: K 147 MET cc_start: 0.8292 (mmp) cc_final: 0.7840 (mtt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1664 time to fit residues: 21.0530 Evaluate side-chains 60 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 0.9990 chunk 120 optimal weight: 40.0000 chunk 129 optimal weight: 30.0000 chunk 138 optimal weight: 40.0000 chunk 118 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 77 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 50.0000 overall best weight: 3.1864 ------------------------------------------------------------------------------- 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 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.035817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.025139 restraints weight = 255877.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.025191 restraints weight = 149186.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025463 restraints weight = 102455.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025540 restraints weight = 82222.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025540 restraints weight = 74485.129| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 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 = 0.2757 r_free = 0.2757 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 (5 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16745 Z= 0.155 Angle : 0.643 8.699 24116 Z= 0.367 Chirality : 0.043 0.239 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.540 177.509 4954 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 703 sheet: -0.52 (0.85), residues: 24 loop : -0.69 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 99 TYR 0.010 0.001 TYR C 57 PHE 0.009 0.001 PHE F 61 TRP 0.007 0.001 TRP L 61 HIS 0.020 0.001 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (16737) covalent geometry : angle 0.64171 / 0.37 (24107) hydrogen bonds : bond 0.04830 / 3.25 ( 896) hydrogen bonds : angle 3.72445 / 2.77 ( 2286) metal coordination : bond 0.00546 / 0.29 ( 8) metal coordination : angle 2.00386 / 1.41 ( 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 87 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.459 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: A 90 MET cc_start: 0.9262 (mmp) cc_final: 0.8995 (mmp) REVERT: A 99 TYR cc_start: 0.9446 (t80) cc_final: 0.9230 (t80) REVERT: A 120 MET cc_start: 0.8471 (mtm) cc_final: 0.8027 (mtp) REVERT: B 49 LEU cc_start: 0.9844 (mp) cc_final: 0.9257 (tt) REVERT: C 95 LYS cc_start: 0.9155 (ptpp) cc_final: 0.8863 (pttp) REVERT: D 102 LEU cc_start: 0.9516 (mm) cc_final: 0.9183 (tp) REVERT: E 120 MET cc_start: 0.8466 (ptp) cc_final: 0.8111 (ptp) REVERT: G 36 LYS cc_start: 0.9478 (ptpp) cc_final: 0.9244 (ptpp) REVERT: G 64 GLU cc_start: 0.9805 (tt0) cc_final: 0.9444 (tm-30) REVERT: G 87 ILE cc_start: 0.9600 (mm) cc_final: 0.9291 (tp) REVERT: G 104 GLN cc_start: 0.9499 (mm-40) cc_final: 0.9171 (mm-40) REVERT: H 59 MET cc_start: 0.9569 (tpt) cc_final: 0.9313 (tpt) REVERT: H 62 MET cc_start: 0.9645 (mmp) cc_final: 0.9308 (mmp) REVERT: H 72 ARG cc_start: 0.9162 (mtt180) cc_final: 0.8909 (mtp85) REVERT: K 38 MET cc_start: 0.9411 (mmp) cc_final: 0.8752 (tpp) REVERT: K 147 MET cc_start: 0.8093 (mmp) cc_final: 0.7469 (mtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1625 time to fit residues: 19.9611 Evaluate side-chains 61 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 40.0000 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.035612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024425 restraints weight = 255114.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024821 restraints weight = 147814.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.025010 restraints weight = 104145.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025247 restraints weight = 88165.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025305 restraints weight = 76634.487| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 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 = 0.2759 r_free = 0.2759 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 (12 function evaluations) r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16745 Z= 0.157 Angle : 0.636 7.227 24116 Z= 0.365 Chirality : 0.043 0.240 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.409 177.237 4954 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.65 (0.19), residues: 703 sheet: -0.34 (0.87), residues: 24 loop : -0.67 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 99 TYR 0.020 0.001 TYR L 64 PHE 0.009 0.001 PHE E 104 TRP 0.005 0.001 TRP L 61 HIS 0.007 0.001 HIS L 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (16737) covalent geometry : angle 0.63526 / 0.36 (24107) hydrogen bonds : bond 0.05012 / 3.38 ( 896) hydrogen bonds : angle 3.71642 / 2.77 ( 2286) metal coordination : bond 0.00584 / 0.32 ( 8) metal coordination : angle 1.91030 / 1.32 ( 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 92 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9261 (mmp) cc_final: 0.8993 (mmp) REVERT: A 99 TYR cc_start: 0.9456 (t80) cc_final: 0.9217 (t80) REVERT: A 120 MET cc_start: 0.8641 (mtm) cc_final: 0.8114 (mtp) REVERT: B 64 ASN cc_start: 0.9708 (m110) cc_final: 0.9493 (m110) REVERT: D 102 LEU cc_start: 0.9519 (mm) cc_final: 0.9211 (tp) REVERT: G 36 LYS cc_start: 0.9456 (ptpp) cc_final: 0.9156 (pttm) REVERT: G 64 GLU cc_start: 0.9795 (tt0) cc_final: 0.9434 (tm-30) REVERT: G 87 ILE cc_start: 0.9588 (mm) cc_final: 0.9246 (tp) REVERT: G 104 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9140 (mm-40) REVERT: H 59 MET cc_start: 0.9573 (tpt) cc_final: 0.9319 (tpt) REVERT: H 62 MET cc_start: 0.9621 (mmp) cc_final: 0.9300 (mmp) REVERT: H 72 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8922 (mtp85) REVERT: K 38 MET cc_start: 0.9457 (mmp) cc_final: 0.8872 (tpp) REVERT: K 147 MET cc_start: 0.8225 (mmp) cc_final: 0.7741 (mtt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1500 time to fit residues: 19.4169 Evaluate side-chains 60 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.035204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.024119 restraints weight = 257352.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024440 restraints weight = 151082.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024599 restraints weight = 105208.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.024826 restraints weight = 90242.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024951 restraints weight = 78451.269| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16745 Z= 0.175 Angle : 0.647 7.558 24116 Z= 0.369 Chirality : 0.042 0.236 2753 Planarity : 0.006 0.111 1880 Dihedral : 31.445 177.394 4954 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 : 0.09 % 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: 1.21 (0.25), residues: 1100 helix: 1.68 (0.19), residues: 686 sheet: -0.30 (0.89), residues: 24 loop : -0.68 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 134 TYR 0.019 0.002 TYR L 64 PHE 0.009 0.001 PHE D 65 TRP 0.005 0.001 TRP L 61 HIS 0.024 0.002 HIS I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (16737) covalent geometry : angle 0.64567 / 0.37 (24107) hydrogen bonds : bond 0.05849 / 3.92 ( 896) hydrogen bonds : angle 3.73998 / 2.78 ( 2286) metal coordination : bond 0.00717 / 0.38 ( 8) metal coordination : angle 1.94399 / 1.34 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.41 seconds wall clock time: 46 minutes 1.22 seconds (2761.22 seconds total)