Starting phenix.real_space_refine on Fri Jan 24 14:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/01_2025/9ipu_60781.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 1, 'ARG: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, 'ASN:plan1': 1, 'ASP:plan': 4} 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, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP: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: 8.95, per 1000 atoms: 0.57 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: 4.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.21 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: 5.70 Time building geometry restraints manager: 4.76 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' DC J 75 " pdb=" N1 DC J 75 " ideal model delta sigma weight residual 1.490 1.391 0.099 3.00e-02 1.11e+03 1.09e+01 bond pdb=" C3' DA N -77 " pdb=" O3' DA N -77 " ideal model delta sigma weight residual 1.422 1.513 -0.091 3.00e-02 1.11e+03 9.14e+00 bond pdb=" C3' DT N -78 " pdb=" O3' DT N -78 " ideal model delta sigma weight residual 1.422 1.511 -0.089 3.00e-02 1.11e+03 8.89e+00 bond pdb=" O5' DG J 79 " pdb=" C5' DG J 79 " ideal model delta sigma weight residual 1.423 1.505 -0.082 3.00e-02 1.11e+03 7.50e+00 bond pdb=" P DT J 77 " pdb=" OP1 DT J 77 " ideal model delta sigma weight residual 1.480 1.534 -0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 22623 2.29 - 4.57: 1354 4.57 - 6.86: 102 6.86 - 9.14: 26 9.14 - 11.43: 2 Bond angle restraints: 24107 Sorted by residual: angle pdb=" C3' DT N 54 " pdb=" O3' DT N 54 " pdb=" P DC N 55 " ideal model delta sigma weight residual 120.20 129.30 -9.10 1.50e+00 4.44e-01 3.68e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 128.82 -8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C3' DG J -58 " pdb=" O3' DG J -58 " pdb=" P DC J -57 " ideal model delta sigma weight residual 120.20 128.79 -8.59 1.50e+00 4.44e-01 3.28e+01 angle pdb=" C4' DA J -54 " pdb=" C3' DA J -54 " pdb=" O3' DA J -54 " ideal model delta sigma weight residual 110.00 101.76 8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 128.35 -8.15 1.50e+00 4.44e-01 2.95e+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 - 0.118: 2636 0.118 - 0.236: 114 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 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 2.47 1.88 0.59 2.00e-01 2.50e+01 8.70e+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 2.42 2.14 0.28 2.00e-01 2.50e+01 2.01e+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 -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.90e+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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.870 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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 : 0.007 0.099 16737 Z= 0.389 Angle : 1.109 11.426 24107 Z= 0.690 Chirality : 0.056 0.590 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP K 93 HIS 0.009 0.001 HIS I 25 PHE 0.051 0.002 PHE I 93 TYR 0.031 0.002 TYR I 28 ARG 0.010 0.000 ARG I 47 *********************** 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 : 1.209 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: 0.9285 (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: 0.2387 (ptt) outliers start: 15 outliers final: 2 residues processed: 218 average time/residue: 0.4161 time to fit residues: 120.7259 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 : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.038775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.027130 restraints weight = 242050.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027720 restraints weight = 136323.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.028144 restraints weight = 94117.962| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16737 Z= 0.340 Angle : 0.744 8.531 24107 Z= 0.431 Chirality : 0.042 0.184 2753 Planarity : 0.006 0.091 1880 Dihedral : 31.242 151.817 4954 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1100 helix: 1.94 (0.20), residues: 695 sheet: -0.47 (0.84), residues: 33 loop : -0.63 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 61 HIS 0.008 0.001 HIS B 75 PHE 0.012 0.002 PHE F 61 TYR 0.017 0.002 TYR E 54 ARG 0.016 0.001 ARG D 92 *********************** 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 132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.122 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: I 31 MET cc_start: 0.8413 (mtm) cc_final: 0.8183 (mtp) REVERT: A 90 MET cc_start: 0.9223 (mmp) cc_final: 0.8833 (mmp) REVERT: A 106 ASP cc_start: 0.9344 (m-30) cc_final: 0.8986 (m-30) REVERT: B 59 LYS cc_start: 0.9599 (tttp) cc_final: 0.9296 (tptp) REVERT: B 63 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9276 (mt-10) REVERT: C 25 PHE cc_start: 0.9257 (m-80) cc_final: 0.8949 (m-80) REVERT: E 106 ASP cc_start: 0.9374 (m-30) cc_final: 0.8790 (m-30) REVERT: H 62 MET cc_start: 0.9632 (mmp) cc_final: 0.9317 (mmm) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.3655 time to fit residues: 64.5892 Evaluate side-chains 73 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 0.0000 chunk 95 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.0028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN H 84 ASN K 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.038571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026945 restraints weight = 240821.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.027572 restraints weight = 132271.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027857 restraints weight = 90687.697| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16737 Z= 0.249 Angle : 0.648 7.967 24107 Z= 0.379 Chirality : 0.039 0.198 2753 Planarity : 0.005 0.050 1880 Dihedral : 31.202 158.863 4954 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1100 helix: 1.82 (0.20), residues: 698 sheet: -0.52 (1.00), residues: 24 loop : -0.59 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 61 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.001 PHE A 104 TYR 0.023 0.002 TYR L 64 ARG 0.012 0.001 ARG A 49 *********************** 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 115 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9185 (mmp) cc_final: 0.8810 (mmp) REVERT: A 106 ASP cc_start: 0.9262 (m-30) cc_final: 0.8772 (m-30) REVERT: B 49 LEU cc_start: 0.9851 (mp) cc_final: 0.9462 (tt) REVERT: B 59 LYS cc_start: 0.9599 (tttp) cc_final: 0.9302 (tptp) REVERT: B 63 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9230 (mt-10) REVERT: C 25 PHE cc_start: 0.9279 (m-80) cc_final: 0.9039 (m-80) REVERT: E 120 MET cc_start: 0.8472 (ptp) cc_final: 0.8237 (ptp) REVERT: G 64 GLU cc_start: 0.9807 (tt0) cc_final: 0.9504 (tm-30) REVERT: G 87 ILE cc_start: 0.9632 (mm) cc_final: 0.9316 (tp) REVERT: H 62 MET cc_start: 0.9642 (mmp) cc_final: 0.9312 (mmp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3544 time to fit residues: 56.7491 Evaluate side-chains 69 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 22 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 102 optimal weight: 50.0000 chunk 114 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.035062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.023765 restraints weight = 261226.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024250 restraints weight = 155078.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024532 restraints weight = 112736.131| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16737 Z= 0.379 Angle : 0.691 7.642 24107 Z= 0.406 Chirality : 0.040 0.158 2753 Planarity : 0.006 0.058 1880 Dihedral : 31.389 179.067 4954 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1100 helix: 1.42 (0.19), residues: 698 sheet: -0.53 (1.00), residues: 24 loop : -0.61 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 93 HIS 0.012 0.002 HIS F 75 PHE 0.013 0.002 PHE F 61 TYR 0.015 0.002 TYR E 54 ARG 0.013 0.001 ARG E 134 *********************** 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 94 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9266 (mmp) cc_final: 0.8972 (mmp) REVERT: B 49 LEU cc_start: 0.9853 (mp) cc_final: 0.9541 (tt) REVERT: B 63 GLU cc_start: 0.9627 (mt-10) cc_final: 0.9354 (mt-10) REVERT: C 25 PHE cc_start: 0.9366 (m-80) cc_final: 0.9104 (m-10) REVERT: D 59 MET cc_start: 0.9140 (tpp) cc_final: 0.8930 (tpp) REVERT: D 68 ASP cc_start: 0.9575 (t70) cc_final: 0.9348 (t0) REVERT: E 64 LYS cc_start: 0.9562 (mppt) cc_final: 0.9359 (mmtm) REVERT: E 120 MET cc_start: 0.8400 (ptp) cc_final: 0.8108 (ptp) REVERT: G 87 ILE cc_start: 0.9643 (mm) cc_final: 0.9342 (tp) REVERT: H 62 MET cc_start: 0.9642 (mmp) cc_final: 0.9349 (mmp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3702 time to fit residues: 48.7255 Evaluate side-chains 67 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 101 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3081 r_free = 0.3081 target = 0.035560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.024195 restraints weight = 257919.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024697 restraints weight = 150987.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024967 restraints weight = 106326.027| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16737 Z= 0.273 Angle : 0.629 7.302 24107 Z= 0.366 Chirality : 0.038 0.168 2753 Planarity : 0.005 0.051 1880 Dihedral : 31.460 179.929 4954 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1100 helix: 1.53 (0.19), residues: 706 sheet: -0.55 (0.97), residues: 24 loop : -0.60 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 61 HIS 0.005 0.001 HIS L 65 PHE 0.010 0.001 PHE E 104 TYR 0.019 0.001 TYR L 64 ARG 0.006 0.001 ARG K 136 *********************** 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 100 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.226 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: 0.9248 (mmp) cc_final: 0.8972 (mmp) REVERT: A 99 TYR cc_start: 0.9539 (t80) cc_final: 0.9331 (t80) REVERT: A 125 GLN cc_start: 0.9636 (mp10) cc_final: 0.9415 (mp10) REVERT: B 49 LEU cc_start: 0.9871 (mp) cc_final: 0.9343 (tt) REVERT: B 59 LYS cc_start: 0.9517 (tptm) cc_final: 0.9313 (tptp) REVERT: C 25 PHE cc_start: 0.9410 (m-80) cc_final: 0.9106 (m-10) REVERT: D 59 MET cc_start: 0.9106 (tpp) cc_final: 0.8861 (tpp) REVERT: D 102 LEU cc_start: 0.9481 (mt) cc_final: 0.9280 (tp) REVERT: E 64 LYS cc_start: 0.9581 (mppt) cc_final: 0.9370 (mmtm) REVERT: E 106 ASP cc_start: 0.9319 (m-30) cc_final: 0.9104 (m-30) REVERT: E 120 MET cc_start: 0.8372 (ptp) cc_final: 0.8068 (ptp) REVERT: G 61 GLU cc_start: 0.9572 (tp30) cc_final: 0.9353 (tp30) REVERT: G 87 ILE cc_start: 0.9621 (mm) cc_final: 0.9300 (tp) REVERT: G 104 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9166 (mm-40) REVERT: H 62 MET cc_start: 0.9646 (mmp) cc_final: 0.9339 (mmp) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.3849 time to fit residues: 53.2097 Evaluate side-chains 74 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 110 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 80 optimal weight: 0.0070 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.034094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.022991 restraints weight = 264850.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.023365 restraints weight = 154864.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.023725 restraints weight = 112949.930| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16737 Z= 0.334 Angle : 0.653 7.383 24107 Z= 0.383 Chirality : 0.038 0.201 2753 Planarity : 0.005 0.058 1880 Dihedral : 31.282 179.725 4954 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1100 helix: 1.42 (0.19), residues: 705 sheet: -0.54 (0.97), residues: 24 loop : -0.73 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 93 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE D 70 TYR 0.013 0.002 TYR D 37 ARG 0.011 0.001 ARG K 136 *********************** 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 89 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9259 (mmp) cc_final: 0.8996 (mmp) REVERT: A 120 MET cc_start: 0.8394 (mtm) cc_final: 0.7840 (mtt) REVERT: D 59 MET cc_start: 0.9080 (tpp) cc_final: 0.8828 (tpp) REVERT: D 71 GLU cc_start: 0.9368 (mp0) cc_final: 0.9085 (mp0) REVERT: D 102 LEU cc_start: 0.9511 (mt) cc_final: 0.9257 (tp) REVERT: E 120 MET cc_start: 0.8653 (ptp) cc_final: 0.8243 (ptp) REVERT: G 61 GLU cc_start: 0.9538 (tp30) cc_final: 0.9198 (tp30) REVERT: G 64 GLU cc_start: 0.9805 (tt0) cc_final: 0.9403 (tm-30) REVERT: G 104 GLN cc_start: 0.9484 (mm-40) cc_final: 0.9149 (mm-40) REVERT: H 62 MET cc_start: 0.9621 (mmp) cc_final: 0.9297 (mmp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3772 time to fit residues: 46.5759 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 : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.035027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023710 restraints weight = 260340.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.024219 restraints weight = 150789.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024367 restraints weight = 108154.578| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16737 Z= 0.226 Angle : 0.613 8.229 24107 Z= 0.356 Chirality : 0.037 0.179 2753 Planarity : 0.005 0.058 1880 Dihedral : 31.246 179.000 4954 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1100 helix: 1.57 (0.19), residues: 706 sheet: -1.10 (0.90), residues: 24 loop : -0.67 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 61 HIS 0.005 0.001 HIS L 65 PHE 0.007 0.001 PHE B 61 TYR 0.023 0.001 TYR L 64 ARG 0.017 0.001 ARG A 134 *********************** 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 97 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.193 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 99 TYR cc_start: 0.9339 (t80) cc_final: 0.8973 (t80) REVERT: B 63 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9105 (tp30) REVERT: C 25 PHE cc_start: 0.9260 (m-80) cc_final: 0.8784 (m-80) REVERT: C 95 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8914 (pttp) REVERT: E 120 MET cc_start: 0.7962 (ptp) cc_final: 0.7652 (ptp) REVERT: G 61 GLU cc_start: 0.9655 (tp30) cc_final: 0.9449 (tp30) REVERT: G 87 ILE cc_start: 0.9107 (mm) cc_final: 0.8839 (tp) REVERT: G 104 GLN cc_start: 0.9649 (mm-40) cc_final: 0.9446 (mm-40) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3823 time to fit residues: 51.0189 Evaluate side-chains 66 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 53 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS H 82 HIS ** 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 = 0.3032 r_free = 0.3032 target = 0.033756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.022820 restraints weight = 262937.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.023186 restraints weight = 155332.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023515 restraints weight = 114014.823| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16737 Z= 0.314 Angle : 0.636 7.313 24107 Z= 0.371 Chirality : 0.038 0.185 2753 Planarity : 0.005 0.060 1880 Dihedral : 31.206 179.319 4954 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1100 helix: 1.49 (0.19), residues: 705 sheet: -1.14 (0.90), residues: 24 loop : -0.76 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 77 HIS 0.005 0.001 HIS D 82 PHE 0.010 0.001 PHE D 65 TYR 0.012 0.002 TYR D 37 ARG 0.007 0.001 ARG A 129 *********************** 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 : 1.499 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: A 90 MET cc_start: 0.9283 (mmp) cc_final: 0.9031 (mmp) REVERT: A 99 TYR cc_start: 0.9455 (t80) cc_final: 0.9241 (t80) REVERT: B 59 LYS cc_start: 0.9543 (tptm) cc_final: 0.9329 (tptp) REVERT: D 37 TYR cc_start: 0.9462 (m-10) cc_final: 0.9168 (m-10) REVERT: E 90 MET cc_start: 0.9396 (mmp) cc_final: 0.9124 (mmp) REVERT: E 120 MET cc_start: 0.8305 (ptp) cc_final: 0.8055 (ptp) REVERT: G 61 GLU cc_start: 0.9519 (tp30) cc_final: 0.9191 (tp30) REVERT: G 64 GLU cc_start: 0.9789 (tt0) cc_final: 0.9396 (tm-30) REVERT: G 104 GLN cc_start: 0.9457 (mm-40) cc_final: 0.9135 (mm-40) REVERT: H 62 MET cc_start: 0.9572 (mmp) cc_final: 0.9251 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3982 time to fit residues: 50.5979 Evaluate side-chains 66 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.023176 restraints weight = 263427.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.023590 restraints weight = 153744.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.023905 restraints weight = 113058.426| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16737 Z= 0.240 Angle : 0.612 7.320 24107 Z= 0.356 Chirality : 0.038 0.252 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.209 179.906 4954 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1100 helix: 1.56 (0.19), residues: 705 sheet: -1.18 (0.90), residues: 24 loop : -0.76 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 61 HIS 0.008 0.001 HIS L 65 PHE 0.012 0.001 PHE A 104 TYR 0.012 0.001 TYR C 57 ARG 0.004 0.000 ARG A 129 *********************** 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 92 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.347 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: 0.9289 (mmp) cc_final: 0.9029 (mmp) REVERT: A 99 TYR cc_start: 0.9475 (t80) cc_final: 0.9233 (t80) REVERT: B 58 LEU cc_start: 0.9912 (tp) cc_final: 0.9624 (pp) REVERT: C 25 PHE cc_start: 0.9364 (m-80) cc_final: 0.9056 (m-10) REVERT: D 37 TYR cc_start: 0.9464 (m-10) cc_final: 0.9049 (m-10) REVERT: D 71 GLU cc_start: 0.9408 (mp0) cc_final: 0.9115 (mp0) REVERT: E 90 MET cc_start: 0.9402 (mmp) cc_final: 0.9120 (mmp) REVERT: E 120 MET cc_start: 0.8182 (ptp) cc_final: 0.7973 (ptp) REVERT: G 36 LYS cc_start: 0.9372 (ptpp) cc_final: 0.9075 (pttm) REVERT: G 61 GLU cc_start: 0.9539 (tp30) cc_final: 0.9210 (tp30) REVERT: G 64 GLU cc_start: 0.9797 (tt0) cc_final: 0.9406 (tm-30) REVERT: G 104 GLN cc_start: 0.9420 (mm-40) cc_final: 0.9107 (mm-40) REVERT: H 62 MET cc_start: 0.9551 (mmp) cc_final: 0.9232 (mmm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4123 time to fit residues: 52.0921 Evaluate side-chains 71 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 GLN B 25 ASN B 75 HIS C 24 GLN D 47 GLN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.034984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.023809 restraints weight = 261150.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.024210 restraints weight = 147374.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024577 restraints weight = 105821.347| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16737 Z= 0.201 Angle : 0.604 7.941 24107 Z= 0.350 Chirality : 0.037 0.186 2753 Planarity : 0.004 0.060 1880 Dihedral : 30.885 179.344 4954 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1100 helix: 1.64 (0.19), residues: 705 sheet: -0.98 (0.88), residues: 29 loop : -0.80 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 61 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 104 TYR 0.018 0.001 TYR L 64 ARG 0.007 0.000 ARG K 136 ********************** 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 94 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.236 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: A 90 MET cc_start: 0.9299 (mmp) cc_final: 0.9063 (mmp) REVERT: B 58 LEU cc_start: 0.9893 (tp) cc_final: 0.9594 (pp) REVERT: B 63 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9332 (mt-10) REVERT: C 25 PHE cc_start: 0.9342 (m-80) cc_final: 0.9093 (m-80) REVERT: D 37 TYR cc_start: 0.9400 (m-10) cc_final: 0.8893 (m-10) REVERT: D 68 ASP cc_start: 0.9564 (t0) cc_final: 0.9357 (t0) REVERT: D 71 GLU cc_start: 0.9414 (mp0) cc_final: 0.9122 (mp0) REVERT: E 90 MET cc_start: 0.9445 (mmp) cc_final: 0.9162 (mmp) REVERT: F 58 LEU cc_start: 0.9829 (tt) cc_final: 0.9616 (pp) REVERT: G 61 GLU cc_start: 0.9558 (tp30) cc_final: 0.9226 (tp30) REVERT: G 64 GLU cc_start: 0.9804 (tt0) cc_final: 0.9413 (tm-30) REVERT: G 104 GLN cc_start: 0.9434 (mm-40) cc_final: 0.9151 (mm-40) REVERT: H 62 MET cc_start: 0.9561 (mmp) cc_final: 0.9236 (mmm) REVERT: H 101 LEU cc_start: 0.9403 (mm) cc_final: 0.9180 (mt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3397 time to fit residues: 45.0804 Evaluate side-chains 73 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.023719 restraints weight = 260040.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024056 restraints weight = 153395.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.024164 restraints weight = 107319.034| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16737 Z= 0.239 Angle : 0.594 7.276 24107 Z= 0.347 Chirality : 0.037 0.196 2753 Planarity : 0.004 0.061 1880 Dihedral : 30.886 178.701 4954 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1100 helix: 1.72 (0.19), residues: 703 sheet: -0.65 (0.80), residues: 38 loop : -0.84 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 141 HIS 0.007 0.001 HIS F 75 PHE 0.016 0.001 PHE A 104 TYR 0.018 0.001 TYR D 37 ARG 0.004 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.92 seconds wall clock time: 86 minutes 10.77 seconds (5170.77 seconds total)