Starting phenix.real_space_refine on Thu Jun 19 02:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/06_2025/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/06_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_60781/06_2025/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/06_2025/9ipu_60781.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/06_2025/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.09, per 1000 atoms: 0.58 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: 3.89 Conformation dependent library (CDL) restraints added in 1.3 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: 7.18 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: 5.63 Time building geometry restraints manager: 4.61 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 43.070 Find NCS groups from input model: 0.400 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- 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 16745 Z= 0.316 Angle : 1.110 11.426 24116 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 Details of bonding type rmsd hydrogen bonds : bond 0.16237 ( 896) hydrogen bonds : angle 6.08603 ( 2286) metal coordination : bond 0.00516 ( 8) metal coordination : angle 2.99243 ( 9) covalent geometry : bond 0.00694 (16737) covalent geometry : angle 1.10891 (24107) *********************** 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 : 1.160 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: 0.4011 time to fit residues: 116.1394 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 : 1.370 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.027146 restraints weight = 242050.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027782 restraints weight = 132868.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028161 restraints weight = 91220.977| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 16745 Z= 0.279 Angle : 0.745 8.531 24116 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 Details of bonding type rmsd hydrogen bonds : bond 0.07585 ( 896) hydrogen bonds : angle 3.69516 ( 2286) metal coordination : bond 0.00807 ( 8) metal coordination : angle 2.58802 ( 9) covalent geometry : bond 0.00614 (16737) covalent geometry : angle 0.74373 (24107) *********************** 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 : 1.578 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: 0.8391 (mtm) cc_final: 0.8170 (mtp) REVERT: A 90 MET cc_start: 0.9182 (mmp) cc_final: 0.8793 (mmp) REVERT: A 106 ASP cc_start: 0.9330 (m-30) cc_final: 0.8950 (m-30) REVERT: B 59 LYS cc_start: 0.9611 (tttp) cc_final: 0.9295 (tptp) REVERT: B 63 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9260 (mt-10) REVERT: C 25 PHE cc_start: 0.9267 (m-80) cc_final: 0.8953 (m-80) REVERT: E 106 ASP cc_start: 0.9339 (m-30) cc_final: 0.8764 (m-30) REVERT: H 62 MET cc_start: 0.9619 (mmp) cc_final: 0.9304 (mmm) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.5730 time to fit residues: 103.4921 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 : 2.369 ------------------------------------------------------------------------------- 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: 30.0000 chunk 42 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.037598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.026047 restraints weight = 245491.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.026598 restraints weight = 138064.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026900 restraints weight = 94219.163| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 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 = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16745 Z= 0.228 Angle : 0.668 7.855 24116 Z= 0.387 Chirality : 0.040 0.199 2753 Planarity : 0.005 0.071 1880 Dihedral : 31.333 160.983 4954 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % 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: 1.25 (0.25), residues: 1100 helix: 1.67 (0.19), residues: 697 sheet: -0.62 (0.99), residues: 24 loop : -0.62 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 93 HIS 0.008 0.001 HIS F 75 PHE 0.017 0.001 PHE A 104 TYR 0.025 0.002 TYR L 64 ARG 0.012 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 896) hydrogen bonds : angle 3.59975 ( 2286) metal coordination : bond 0.00494 ( 8) metal coordination : angle 2.49935 ( 9) covalent geometry : bond 0.00499 (16737) covalent geometry : angle 0.66654 (24107) *********************** 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 118 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.519 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: I 31 MET cc_start: 0.8282 (mtm) cc_final: 0.8062 (mtm) REVERT: A 90 MET cc_start: 0.9183 (mmp) cc_final: 0.8801 (mmp) REVERT: A 106 ASP cc_start: 0.9291 (m-30) cc_final: 0.8812 (m-30) REVERT: B 49 LEU cc_start: 0.9849 (mp) cc_final: 0.9441 (tt) REVERT: B 59 LYS cc_start: 0.9619 (tttp) cc_final: 0.9342 (tptp) REVERT: B 63 GLU cc_start: 0.9634 (mt-10) cc_final: 0.9257 (mt-10) REVERT: C 25 PHE cc_start: 0.9299 (m-80) cc_final: 0.9096 (m-80) REVERT: D 59 MET cc_start: 0.9060 (tpp) cc_final: 0.8843 (tpp) REVERT: E 64 LYS cc_start: 0.9510 (mppt) cc_final: 0.9294 (mmtm) REVERT: E 120 MET cc_start: 0.8605 (ptp) cc_final: 0.8269 (ptp) REVERT: G 64 GLU cc_start: 0.9800 (tt0) cc_final: 0.9491 (tm-30) REVERT: G 87 ILE cc_start: 0.9637 (mm) cc_final: 0.9332 (tp) REVERT: H 62 MET cc_start: 0.9635 (mmp) cc_final: 0.9314 (mmp) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.4048 time to fit residues: 65.7133 Evaluate side-chains 73 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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: 4.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025193 restraints weight = 251495.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025700 restraints weight = 144435.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.026062 restraints weight = 102391.194| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16745 Z= 0.225 Angle : 0.628 7.395 24116 Z= 0.369 Chirality : 0.037 0.189 2753 Planarity : 0.005 0.065 1880 Dihedral : 31.135 179.729 4954 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 1.36 (0.25), residues: 1100 helix: 1.73 (0.19), residues: 700 sheet: -0.44 (0.97), residues: 24 loop : -0.55 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 77 HIS 0.009 0.001 HIS F 75 PHE 0.010 0.002 PHE A 104 TYR 0.012 0.002 TYR C 50 ARG 0.010 0.001 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.05918 ( 896) hydrogen bonds : angle 3.49464 ( 2286) metal coordination : bond 0.00484 ( 8) metal coordination : angle 2.11250 ( 9) covalent geometry : bond 0.00491 (16737) covalent geometry : angle 0.62697 (24107) *********************** 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 104 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.130 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: 0.9200 (mmp) cc_final: 0.8903 (mmp) REVERT: B 49 LEU cc_start: 0.9860 (mp) cc_final: 0.9566 (tt) REVERT: B 59 LYS cc_start: 0.9622 (tttp) cc_final: 0.9332 (tptp) REVERT: B 63 GLU cc_start: 0.9607 (mt-10) cc_final: 0.9184 (mt-10) REVERT: C 25 PHE cc_start: 0.9308 (m-80) cc_final: 0.9039 (m-10) REVERT: D 59 MET cc_start: 0.9138 (tpp) cc_final: 0.8866 (tpp) REVERT: D 71 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9065 (mt-10) REVERT: E 120 MET cc_start: 0.8345 (ptp) cc_final: 0.8069 (ptp) REVERT: G 87 ILE cc_start: 0.9608 (mm) cc_final: 0.9301 (tp) REVERT: H 62 MET cc_start: 0.9645 (mmp) cc_final: 0.9312 (mmp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3361 time to fit residues: 49.3869 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 : 1.175 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 83 optimal weight: 40.0000 chunk 45 optimal weight: 6.9990 overall best weight: 3.2404 ------------------------------------------------------------------------------- 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 ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 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 = 0.3111 r_free = 0.3111 target = 0.036581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.025214 restraints weight = 247887.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025710 restraints weight = 141302.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026052 restraints weight = 102014.753| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16745 Z= 0.188 Angle : 0.601 7.245 24116 Z= 0.351 Chirality : 0.037 0.163 2753 Planarity : 0.004 0.062 1880 Dihedral : 31.054 179.239 4954 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % 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: 1.40 (0.26), residues: 1100 helix: 1.75 (0.19), residues: 708 sheet: -0.42 (1.00), residues: 24 loop : -0.57 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 61 HIS 0.008 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.019 0.001 TYR L 64 ARG 0.011 0.000 ARG K 139 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 896) hydrogen bonds : angle 3.43479 ( 2286) metal coordination : bond 0.00416 ( 8) metal coordination : angle 1.68069 ( 9) covalent geometry : bond 0.00411 (16737) covalent geometry : angle 0.60032 (24107) *********************** 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 104 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.198 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: 0.9293 (mmp) cc_final: 0.9002 (mmp) REVERT: A 99 TYR cc_start: 0.9517 (t80) cc_final: 0.9302 (t80) REVERT: B 49 LEU cc_start: 0.9873 (mp) cc_final: 0.9430 (tt) REVERT: B 63 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9383 (mp0) REVERT: C 25 PHE cc_start: 0.9399 (m-80) cc_final: 0.9152 (m-80) REVERT: D 59 MET cc_start: 0.9159 (tpp) cc_final: 0.8884 (tpp) REVERT: D 71 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9062 (mt-10) REVERT: D 102 LEU cc_start: 0.9473 (mt) cc_final: 0.9264 (tp) REVERT: E 64 LYS cc_start: 0.9531 (mppt) cc_final: 0.9293 (mmtm) REVERT: E 120 MET cc_start: 0.8308 (ptp) cc_final: 0.8015 (ptp) REVERT: G 87 ILE cc_start: 0.9596 (mm) cc_final: 0.9281 (tp) REVERT: G 104 GLN cc_start: 0.9518 (mm-40) cc_final: 0.9183 (mm-40) REVERT: H 59 MET cc_start: 0.9580 (tpt) cc_final: 0.9374 (tpt) REVERT: H 62 MET cc_start: 0.9675 (mmp) cc_final: 0.9343 (mmp) REVERT: K 147 MET cc_start: 0.8142 (mmp) cc_final: 0.7291 (mpp) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.3435 time to fit residues: 49.6827 Evaluate side-chains 71 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 20.0000 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 110 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.0010 chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 80 optimal weight: 0.3980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 GLN D 109 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 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 = 0.3121 r_free = 0.3121 target = 0.037071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.025446 restraints weight = 251352.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.025972 restraints weight = 142877.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.026397 restraints weight = 101347.815| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5096 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= 0.159 Angle : 0.590 7.278 24116 Z= 0.344 Chirality : 0.036 0.165 2753 Planarity : 0.004 0.059 1880 Dihedral : 30.782 178.655 4954 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.49 (0.26), residues: 1100 helix: 1.80 (0.20), residues: 706 sheet: -0.14 (1.01), residues: 24 loop : -0.48 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 61 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 104 TYR 0.011 0.001 TYR C 57 ARG 0.025 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 896) hydrogen bonds : angle 3.36753 ( 2286) metal coordination : bond 0.00312 ( 8) metal coordination : angle 1.48712 ( 9) covalent geometry : bond 0.00347 (16737) covalent geometry : angle 0.58943 (24107) *********************** 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 101 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.825 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: 0.9329 (mmp) cc_final: 0.9035 (mmp) REVERT: A 99 TYR cc_start: 0.9462 (t80) cc_final: 0.9242 (t80) REVERT: B 49 LEU cc_start: 0.9863 (mp) cc_final: 0.9545 (tt) REVERT: C 25 PHE cc_start: 0.9366 (m-80) cc_final: 0.9031 (m-10) REVERT: C 79 ILE cc_start: 0.9752 (tp) cc_final: 0.9548 (pt) REVERT: D 59 MET cc_start: 0.9131 (tpp) cc_final: 0.8825 (tpp) REVERT: D 68 ASP cc_start: 0.9638 (t70) cc_final: 0.9432 (t0) REVERT: D 71 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9002 (mt-10) REVERT: D 102 LEU cc_start: 0.9457 (mt) cc_final: 0.9211 (tp) REVERT: E 64 LYS cc_start: 0.9506 (mppt) cc_final: 0.9302 (mmtm) REVERT: E 120 MET cc_start: 0.8271 (ptp) cc_final: 0.8013 (ptp) REVERT: G 64 GLU cc_start: 0.9808 (tt0) cc_final: 0.9494 (tm-30) REVERT: G 87 ILE cc_start: 0.9584 (mm) cc_final: 0.9251 (tp) REVERT: G 104 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9143 (mm-40) REVERT: H 62 MET cc_start: 0.9657 (mmp) cc_final: 0.9321 (mmp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4473 time to fit residues: 63.4482 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 : 1.645 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.036316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025402 restraints weight = 254364.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025452 restraints weight = 154141.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.025653 restraints weight = 105717.840| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 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 = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16745 Z= 0.185 Angle : 0.612 17.883 24116 Z= 0.350 Chirality : 0.037 0.372 2753 Planarity : 0.004 0.058 1880 Dihedral : 30.673 179.804 4954 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.25), residues: 1100 helix: 1.79 (0.19), residues: 708 sheet: -0.03 (1.03), residues: 24 loop : -0.58 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.014 0.001 TYR L 64 ARG 0.011 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 896) hydrogen bonds : angle 3.41272 ( 2286) metal coordination : bond 0.00431 ( 8) metal coordination : angle 1.53979 ( 9) covalent geometry : bond 0.00403 (16737) covalent geometry : angle 0.61102 (24107) *********************** 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 103 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9315 (mmp) cc_final: 0.9039 (mmp) REVERT: A 99 TYR cc_start: 0.9487 (t80) cc_final: 0.9251 (t80) REVERT: A 120 MET cc_start: 0.8354 (mtm) cc_final: 0.7814 (mtt) REVERT: C 95 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8844 (pttp) REVERT: D 59 MET cc_start: 0.9124 (tpp) cc_final: 0.8819 (tpp) REVERT: D 68 ASP cc_start: 0.9627 (t70) cc_final: 0.9421 (t0) REVERT: D 71 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8987 (mt-10) REVERT: D 102 LEU cc_start: 0.9463 (mt) cc_final: 0.9219 (tp) REVERT: E 64 LYS cc_start: 0.9570 (mppt) cc_final: 0.9363 (mmtm) REVERT: E 120 MET cc_start: 0.8548 (ptp) cc_final: 0.8179 (ptp) REVERT: G 87 ILE cc_start: 0.9576 (mm) cc_final: 0.9254 (tp) REVERT: G 104 GLN cc_start: 0.9510 (mm-40) cc_final: 0.9165 (mm-40) REVERT: H 62 MET cc_start: 0.9655 (mmp) cc_final: 0.9335 (mmp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3671 time to fit residues: 52.8611 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 : 1.144 ------------------------------------------------------------------------------- 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: 6.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.024838 restraints weight = 253781.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025229 restraints weight = 149425.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.025614 restraints weight = 106716.998| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16745 Z= 0.178 Angle : 0.607 14.126 24116 Z= 0.348 Chirality : 0.037 0.349 2753 Planarity : 0.004 0.059 1880 Dihedral : 30.657 179.832 4954 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 1.49 (0.26), residues: 1100 helix: 1.84 (0.20), residues: 707 sheet: -0.05 (1.02), residues: 24 loop : -0.60 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 61 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE C 25 TYR 0.018 0.001 TYR L 64 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 896) hydrogen bonds : angle 3.41151 ( 2286) metal coordination : bond 0.00314 ( 8) metal coordination : angle 1.57902 ( 9) covalent geometry : bond 0.00389 (16737) covalent geometry : angle 0.60622 (24107) *********************** 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 98 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.297 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: 0.9326 (mmp) cc_final: 0.9053 (mmp) REVERT: A 99 TYR cc_start: 0.9495 (t80) cc_final: 0.9219 (t80) REVERT: B 49 LEU cc_start: 0.9856 (mp) cc_final: 0.9348 (tt) REVERT: D 37 TYR cc_start: 0.9412 (m-10) cc_final: 0.9161 (m-10) REVERT: D 59 MET cc_start: 0.9153 (tpp) cc_final: 0.8866 (tpp) REVERT: D 68 ASP cc_start: 0.9619 (t70) cc_final: 0.9412 (t0) REVERT: D 71 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8977 (mt-10) REVERT: D 102 LEU cc_start: 0.9432 (mt) cc_final: 0.9174 (tp) REVERT: E 105 GLU cc_start: 0.9603 (pm20) cc_final: 0.9401 (pm20) REVERT: G 36 LYS cc_start: 0.9495 (pttp) cc_final: 0.9235 (pttm) REVERT: G 64 GLU cc_start: 0.9800 (tt0) cc_final: 0.9487 (tm-30) REVERT: G 87 ILE cc_start: 0.9558 (mm) cc_final: 0.9225 (tp) REVERT: G 104 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9154 (mm-40) REVERT: H 59 MET cc_start: 0.9587 (tpt) cc_final: 0.9332 (tpt) REVERT: H 62 MET cc_start: 0.9661 (mmp) cc_final: 0.9344 (mmp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3403 time to fit residues: 48.0950 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 : 1.137 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.036005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.025263 restraints weight = 255190.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.025275 restraints weight = 145106.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025520 restraints weight = 101092.438| |-----------------------------------------------------------------------------| 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: 11 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16745 Z= 0.174 Angle : 0.596 14.483 24116 Z= 0.343 Chirality : 0.036 0.345 2753 Planarity : 0.005 0.075 1880 Dihedral : 30.578 179.351 4954 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.50 (0.25), residues: 1100 helix: 1.84 (0.19), residues: 707 sheet: 0.05 (1.02), residues: 24 loop : -0.59 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE C 25 TYR 0.014 0.001 TYR F 72 ARG 0.003 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 896) hydrogen bonds : angle 3.38891 ( 2286) metal coordination : bond 0.00321 ( 8) metal coordination : angle 1.53974 ( 9) covalent geometry : bond 0.00379 (16737) covalent geometry : angle 0.59494 (24107) *********************** 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 99 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.359 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: 0.9024 (mmp) REVERT: A 99 TYR cc_start: 0.9459 (t80) cc_final: 0.9180 (t80) REVERT: D 37 TYR cc_start: 0.9306 (m-10) cc_final: 0.9040 (m-10) REVERT: D 59 MET cc_start: 0.9128 (tpp) cc_final: 0.8823 (tpp) REVERT: D 68 ASP cc_start: 0.9597 (t70) cc_final: 0.9386 (t0) REVERT: D 71 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8957 (mt-10) REVERT: D 102 LEU cc_start: 0.9459 (mt) cc_final: 0.9201 (tp) REVERT: G 64 GLU cc_start: 0.9793 (tt0) cc_final: 0.9457 (tm-30) REVERT: G 87 ILE cc_start: 0.9588 (mm) cc_final: 0.9256 (tp) REVERT: G 104 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9143 (mm-40) REVERT: H 62 MET cc_start: 0.9612 (mmp) cc_final: 0.9340 (mmp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3442 time to fit residues: 48.2575 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 : 1.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 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: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.034933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023666 restraints weight = 264721.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.024057 restraints weight = 151961.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024525 restraints weight = 110794.264| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16745 Z= 0.220 Angle : 0.619 12.745 24116 Z= 0.358 Chirality : 0.038 0.331 2753 Planarity : 0.005 0.099 1880 Dihedral : 30.705 178.913 4954 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: 1.37 (0.25), residues: 1100 helix: 1.74 (0.19), residues: 707 sheet: 0.03 (1.00), residues: 24 loop : -0.65 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 93 HIS 0.010 0.001 HIS L 65 PHE 0.010 0.001 PHE B 61 TYR 0.021 0.002 TYR L 64 ARG 0.006 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.05889 ( 896) hydrogen bonds : angle 3.57626 ( 2286) metal coordination : bond 0.00587 ( 8) metal coordination : angle 1.72762 ( 9) covalent geometry : bond 0.00479 (16737) covalent geometry : angle 0.61854 (24107) ********************** 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 : 1.240 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 99 TYR cc_start: 0.9268 (t80) cc_final: 0.8943 (t80) REVERT: D 37 TYR cc_start: 0.9618 (m-10) cc_final: 0.9394 (m-10) REVERT: G 61 GLU cc_start: 0.9648 (tp30) cc_final: 0.9345 (tp30) REVERT: H 62 MET cc_start: 0.9879 (mmp) cc_final: 0.9656 (mmm) REVERT: H 101 LEU cc_start: 0.8585 (mm) cc_final: 0.8286 (mp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3292 time to fit residues: 43.9727 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 : 1.336 ------------------------------------------------------------------------------- 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: 0.5980 chunk 86 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.035693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.024439 restraints weight = 255994.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024958 restraints weight = 148932.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.025141 restraints weight = 106880.796| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16745 Z= 0.163 Angle : 0.609 13.225 24116 Z= 0.350 Chirality : 0.037 0.318 2753 Planarity : 0.005 0.074 1880 Dihedral : 30.606 179.160 4954 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 1.40 (0.26), residues: 1100 helix: 1.77 (0.19), residues: 707 sheet: 0.05 (0.99), residues: 24 loop : -0.64 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 61 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE C 25 TYR 0.019 0.001 TYR L 64 ARG 0.006 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 896) hydrogen bonds : angle 3.49406 ( 2286) metal coordination : bond 0.00374 ( 8) metal coordination : angle 1.62864 ( 9) covalent geometry : bond 0.00354 (16737) covalent geometry : angle 0.60859 (24107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5477.82 seconds wall clock time: 99 minutes 4.35 seconds (5944.35 seconds total)