Starting phenix.real_space_refine on Wed May 21 21:32:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/05_2025/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/05_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_60781/05_2025/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/05_2025/9ipu_60781.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/05_2025/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 15750 Number of models: 1 Model: "" Number of chains: 15 Chain: "I" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 526 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1125 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 407 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 55} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3488 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "N" Number of atoms: 3484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3484 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7931 SG CYS L 31 64.159 100.830 26.967 1.00218.04 S ATOM 8073 SG CYS L 51 66.529 103.652 27.672 1.00210.14 S ATOM 8097 SG CYS L 54 63.002 104.560 26.813 1.00213.50 S ATOM 7822 SG CYS L 16 75.394 98.933 21.484 1.00283.03 S ATOM 7840 SG CYS L 19 78.982 98.250 20.552 1.00282.47 S ATOM 7970 SG CYS L 36 77.356 96.060 23.117 1.00253.66 S ATOM 7988 SG CYS L 39 78.088 99.560 24.108 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 8.88, per 1000 atoms: 0.56 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: 3.88 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: 7.01 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: 5.73 Time building geometry restraints manager: 4.54 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 42.530 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.880 ------------------------------------------------------------------------------- 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 : 1.176 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: 0.3879 time to fit residues: 113.0020 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 : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.038775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.027130 restraints weight = 242050.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027720 restraints weight = 136323.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.028144 restraints weight = 94117.962| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 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 : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 31 MET cc_start: 0.8413 (mtm) cc_final: 0.8183 (mtp) REVERT: A 90 MET cc_start: 0.9223 (mmp) cc_final: 0.8833 (mmp) REVERT: A 106 ASP cc_start: 0.9344 (m-30) cc_final: 0.8986 (m-30) REVERT: B 59 LYS cc_start: 0.9599 (tttp) cc_final: 0.9296 (tptp) REVERT: B 63 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9276 (mt-10) REVERT: C 25 PHE cc_start: 0.9257 (m-80) cc_final: 0.8949 (m-80) REVERT: E 106 ASP cc_start: 0.9374 (m-30) cc_final: 0.8790 (m-30) REVERT: H 62 MET cc_start: 0.9632 (mmp) cc_final: 0.9317 (mmm) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.3732 time to fit residues: 66.4671 Evaluate side-chains 73 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.0000 chunk 95 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN H 84 ASN K 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.038051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.026431 restraints weight = 242199.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.027003 restraints weight = 135027.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.027244 restraints weight = 93585.410| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 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 = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16745 Z= 0.221 Angle : 0.657 8.179 24116 Z= 0.384 Chirality : 0.039 0.209 2753 Planarity : 0.005 0.054 1880 Dihedral : 31.260 159.584 4954 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % 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: 1.37 (0.25), residues: 1100 helix: 1.77 (0.19), residues: 697 sheet: -0.62 (0.99), residues: 24 loop : -0.60 (0.32), residues: 379 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 0.013 0.001 PHE A 104 TYR 0.022 0.002 TYR L 64 ARG 0.011 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 896) hydrogen bonds : angle 3.53567 ( 2286) metal coordination : bond 0.00484 ( 8) metal coordination : angle 2.44228 ( 9) covalent geometry : bond 0.00480 (16737) covalent geometry : angle 0.65589 (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 115 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9192 (mmp) cc_final: 0.8819 (mmp) REVERT: A 106 ASP cc_start: 0.9292 (m-30) cc_final: 0.8785 (m-30) REVERT: B 49 LEU cc_start: 0.9852 (mp) cc_final: 0.9461 (tt) REVERT: B 59 LYS cc_start: 0.9605 (tttp) cc_final: 0.9308 (tptp) REVERT: B 63 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9235 (mt-10) REVERT: C 25 PHE cc_start: 0.9288 (m-80) cc_final: 0.9064 (m-80) REVERT: E 64 LYS cc_start: 0.9459 (mppt) cc_final: 0.9247 (mmtm) REVERT: E 120 MET cc_start: 0.8630 (ptp) cc_final: 0.8328 (ptp) REVERT: G 64 GLU cc_start: 0.9802 (tt0) cc_final: 0.9503 (tm-30) REVERT: G 87 ILE cc_start: 0.9629 (mm) cc_final: 0.9318 (tp) REVERT: H 62 MET cc_start: 0.9636 (mmp) cc_final: 0.9309 (mmp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3403 time to fit residues: 54.4448 Evaluate side-chains 72 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 22 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.034860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.023804 restraints weight = 262689.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.024103 restraints weight = 159515.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.024383 restraints weight = 112268.675| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16745 Z= 0.332 Angle : 0.699 7.432 24116 Z= 0.409 Chirality : 0.040 0.184 2753 Planarity : 0.006 0.068 1880 Dihedral : 31.489 179.017 4954 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1100 helix: 1.39 (0.19), residues: 698 sheet: -0.63 (0.97), residues: 24 loop : -0.63 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 93 HIS 0.008 0.002 HIS B 75 PHE 0.014 0.002 PHE A 104 TYR 0.016 0.002 TYR E 54 ARG 0.008 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.10153 ( 896) hydrogen bonds : angle 3.90318 ( 2286) metal coordination : bond 0.00797 ( 8) metal coordination : angle 2.51660 ( 9) covalent geometry : bond 0.00723 (16737) covalent geometry : angle 0.69744 (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 96 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9223 (mmp) cc_final: 0.8938 (mmp) REVERT: B 49 LEU cc_start: 0.9862 (mp) cc_final: 0.9545 (tt) REVERT: B 59 LYS cc_start: 0.9664 (tttp) cc_final: 0.9378 (tppp) REVERT: B 63 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9300 (mp0) REVERT: C 25 PHE cc_start: 0.9375 (m-80) cc_final: 0.9121 (m-10) REVERT: D 59 MET cc_start: 0.9115 (tpp) cc_final: 0.8897 (tpp) REVERT: D 68 ASP cc_start: 0.9536 (t70) cc_final: 0.9320 (t0) REVERT: E 120 MET cc_start: 0.8439 (ptp) cc_final: 0.8156 (ptp) REVERT: G 87 ILE cc_start: 0.9657 (mm) cc_final: 0.9357 (tp) REVERT: H 62 MET cc_start: 0.9643 (mmp) cc_final: 0.9336 (mmp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3405 time to fit residues: 46.1417 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 : 1.249 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.036399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.025033 restraints weight = 250632.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.025543 restraints weight = 143638.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025912 restraints weight = 101895.554| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16745 Z= 0.174 Angle : 0.614 7.238 24116 Z= 0.356 Chirality : 0.037 0.165 2753 Planarity : 0.005 0.055 1880 Dihedral : 31.423 179.404 4954 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.11 % Allowed : 1.96 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.25), residues: 1100 helix: 1.63 (0.19), residues: 706 sheet: -0.40 (0.97), residues: 24 loop : -0.63 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 61 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.001 PHE E 104 TYR 0.025 0.001 TYR L 64 ARG 0.010 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 896) hydrogen bonds : angle 3.53597 ( 2286) metal coordination : bond 0.00410 ( 8) metal coordination : angle 1.82888 ( 9) covalent geometry : bond 0.00378 (16737) covalent geometry : angle 0.61276 (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 103 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9259 (mmp) cc_final: 0.8973 (mmp) REVERT: A 99 TYR cc_start: 0.9530 (t80) cc_final: 0.9322 (t80) REVERT: B 49 LEU cc_start: 0.9883 (mp) cc_final: 0.9562 (tt) REVERT: C 25 PHE cc_start: 0.9425 (m-80) cc_final: 0.9171 (m-80) REVERT: D 59 MET cc_start: 0.9075 (tpp) cc_final: 0.8814 (tpp) REVERT: D 102 LEU cc_start: 0.9454 (mt) cc_final: 0.9243 (tp) REVERT: E 64 LYS cc_start: 0.9519 (mppt) cc_final: 0.9297 (mmtm) REVERT: E 120 MET cc_start: 0.8395 (ptp) cc_final: 0.8099 (ptp) REVERT: G 61 GLU cc_start: 0.9572 (tp30) cc_final: 0.9363 (tp30) REVERT: G 87 ILE cc_start: 0.9620 (mm) cc_final: 0.9289 (tp) REVERT: G 104 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9143 (mm-40) REVERT: H 59 MET cc_start: 0.9577 (tpt) cc_final: 0.9352 (tpt) REVERT: H 62 MET cc_start: 0.9634 (mmp) cc_final: 0.9318 (mmp) REVERT: H 72 ARG cc_start: 0.9201 (mtt180) cc_final: 0.8916 (mtp85) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.3615 time to fit residues: 51.6362 Evaluate side-chains 72 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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: 0.9990 chunk 104 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 110 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 80 optimal weight: 0.0170 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.035962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024602 restraints weight = 256296.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.025082 restraints weight = 146225.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.025390 restraints weight = 104684.118| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16745 Z= 0.190 Angle : 0.599 7.322 24116 Z= 0.349 Chirality : 0.037 0.170 2753 Planarity : 0.004 0.057 1880 Dihedral : 31.102 178.439 4954 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 1.33 (0.26), residues: 1100 helix: 1.73 (0.19), residues: 707 sheet: -0.39 (0.96), residues: 24 loop : -0.66 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 61 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.010 0.001 TYR H 40 ARG 0.004 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 896) hydrogen bonds : angle 3.48034 ( 2286) metal coordination : bond 0.00440 ( 8) metal coordination : angle 1.68287 ( 9) covalent geometry : bond 0.00414 (16737) covalent geometry : angle 0.59780 (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 98 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.237 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: 0.9279 (mmp) cc_final: 0.9007 (mmp) REVERT: A 99 TYR cc_start: 0.9536 (t80) cc_final: 0.9318 (t80) REVERT: B 49 LEU cc_start: 0.9866 (mp) cc_final: 0.9308 (tt) REVERT: B 63 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9391 (mp0) REVERT: C 25 PHE cc_start: 0.9373 (m-80) cc_final: 0.9160 (m-80) REVERT: D 59 MET cc_start: 0.9077 (tpp) cc_final: 0.8807 (tpp) REVERT: D 102 LEU cc_start: 0.9473 (mt) cc_final: 0.9233 (tp) REVERT: E 64 LYS cc_start: 0.9528 (mppt) cc_final: 0.9305 (mmtm) REVERT: E 120 MET cc_start: 0.8537 (ptp) cc_final: 0.8223 (ptp) REVERT: G 87 ILE cc_start: 0.9611 (mm) cc_final: 0.9275 (tp) REVERT: G 104 GLN cc_start: 0.9464 (mm-40) cc_final: 0.9140 (mm-40) REVERT: H 62 MET cc_start: 0.9649 (mmp) cc_final: 0.9321 (mmp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3705 time to fit residues: 50.0362 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 : 1.437 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.023385 restraints weight = 261455.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.023827 restraints weight = 155073.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024170 restraints weight = 111564.179| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16745 Z= 0.278 Angle : 0.662 17.858 24116 Z= 0.381 Chirality : 0.039 0.421 2753 Planarity : 0.005 0.060 1880 Dihedral : 31.143 179.783 4954 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.09 (0.25), residues: 1100 helix: 1.54 (0.19), residues: 705 sheet: -1.21 (0.87), residues: 24 loop : -0.67 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 93 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.002 PHE F 61 TYR 0.016 0.002 TYR F 72 ARG 0.009 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.07805 ( 896) hydrogen bonds : angle 3.76511 ( 2286) metal coordination : bond 0.00815 ( 8) metal coordination : angle 2.07450 ( 9) covalent geometry : bond 0.00606 (16737) covalent geometry : angle 0.66129 (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 91 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.190 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 74 ILE cc_start: 0.9744 (tp) cc_final: 0.9529 (tp) REVERT: A 90 MET cc_start: 0.9274 (mmp) cc_final: 0.9009 (mmp) REVERT: A 99 TYR cc_start: 0.9542 (t80) cc_final: 0.9261 (t80) REVERT: A 120 MET cc_start: 0.8381 (mtm) cc_final: 0.7769 (mtt) REVERT: B 59 LYS cc_start: 0.9632 (tttp) cc_final: 0.9381 (tptm) REVERT: C 25 PHE cc_start: 0.9402 (m-80) cc_final: 0.9189 (m-80) REVERT: D 59 MET cc_start: 0.9081 (tpp) cc_final: 0.8827 (tpp) REVERT: D 102 LEU cc_start: 0.9467 (mt) cc_final: 0.9208 (tp) REVERT: E 90 MET cc_start: 0.9432 (mmp) cc_final: 0.9132 (mmp) REVERT: E 120 MET cc_start: 0.8406 (ptp) cc_final: 0.8148 (ptp) REVERT: G 64 GLU cc_start: 0.9816 (tt0) cc_final: 0.9455 (tm-30) REVERT: G 87 ILE cc_start: 0.9632 (mm) cc_final: 0.9302 (tp) REVERT: G 104 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9153 (mm-40) REVERT: H 62 MET cc_start: 0.9626 (mmp) cc_final: 0.9304 (mmp) REVERT: M 32 ASP cc_start: 0.6514 (t0) cc_final: 0.5962 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3516 time to fit residues: 44.3497 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 : 1.304 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 6.9990 chunk 93 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- 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 ** 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 = 0.3074 r_free = 0.3074 target = 0.035449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.024114 restraints weight = 257483.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024536 restraints weight = 149345.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.024770 restraints weight = 109074.573| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16745 Z= 0.182 Angle : 0.617 13.140 24116 Z= 0.355 Chirality : 0.038 0.369 2753 Planarity : 0.005 0.068 1880 Dihedral : 31.070 179.319 4954 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1100 helix: 1.58 (0.19), residues: 706 sheet: -0.95 (0.92), residues: 24 loop : -0.68 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 61 HIS 0.006 0.001 HIS L 65 PHE 0.007 0.001 PHE F 61 TYR 0.031 0.002 TYR L 64 ARG 0.004 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 896) hydrogen bonds : angle 3.60400 ( 2286) metal coordination : bond 0.00524 ( 8) metal coordination : angle 1.82431 ( 9) covalent geometry : bond 0.00399 (16737) covalent geometry : angle 0.61652 (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 : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9308 (mmp) cc_final: 0.9039 (mmp) REVERT: A 99 TYR cc_start: 0.9521 (t80) cc_final: 0.9237 (t80) REVERT: A 120 MET cc_start: 0.8277 (mtm) cc_final: 0.7994 (mtp) REVERT: B 63 GLU cc_start: 0.9607 (mt-10) cc_final: 0.9358 (mt-10) REVERT: C 25 PHE cc_start: 0.9347 (m-80) cc_final: 0.9126 (m-80) REVERT: C 95 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8867 (pttp) REVERT: D 37 TYR cc_start: 0.9454 (m-10) cc_final: 0.9094 (m-10) REVERT: D 59 MET cc_start: 0.9118 (tpp) cc_final: 0.8847 (tpp) REVERT: D 102 LEU cc_start: 0.9451 (mt) cc_final: 0.9208 (tp) REVERT: E 120 MET cc_start: 0.8199 (ptp) cc_final: 0.7989 (ptp) REVERT: G 61 GLU cc_start: 0.9548 (tp30) cc_final: 0.9223 (tp30) REVERT: G 64 GLU cc_start: 0.9815 (tt0) cc_final: 0.9420 (tm-30) REVERT: G 87 ILE cc_start: 0.9564 (mm) cc_final: 0.9286 (tp) REVERT: G 104 GLN cc_start: 0.9487 (mm-40) cc_final: 0.9148 (mm-40) REVERT: H 62 MET cc_start: 0.9659 (mmp) cc_final: 0.9349 (mmp) REVERT: M 32 ASP cc_start: 0.6522 (t0) cc_final: 0.5970 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3988 time to fit residues: 55.4690 Evaluate side-chains 68 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.024227 restraints weight = 258408.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024654 restraints weight = 148355.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.024794 restraints weight = 108110.488| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.6248 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= 0.172 Angle : 0.604 13.770 24116 Z= 0.347 Chirality : 0.037 0.328 2753 Planarity : 0.004 0.061 1880 Dihedral : 30.805 179.474 4954 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.26), residues: 1100 helix: 1.70 (0.19), residues: 706 sheet: -0.84 (0.93), residues: 24 loop : -0.68 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 77 HIS 0.006 0.001 HIS G 31 PHE 0.010 0.001 PHE A 104 TYR 0.015 0.001 TYR F 72 ARG 0.006 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 896) hydrogen bonds : angle 3.51786 ( 2286) metal coordination : bond 0.00656 ( 8) metal coordination : angle 3.73396 ( 9) covalent geometry : bond 0.00376 (16737) covalent geometry : angle 0.59939 (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 95 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.207 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: 0.9332 (mmp) cc_final: 0.9059 (mmp) REVERT: A 99 TYR cc_start: 0.9502 (t80) cc_final: 0.9195 (t80) REVERT: B 63 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9352 (mt-10) REVERT: C 25 PHE cc_start: 0.9316 (m-80) cc_final: 0.9097 (m-80) REVERT: D 37 TYR cc_start: 0.9437 (m-10) cc_final: 0.9023 (m-10) REVERT: D 59 MET cc_start: 0.9114 (tpp) cc_final: 0.8854 (tpp) REVERT: D 102 LEU cc_start: 0.9483 (mt) cc_final: 0.9221 (tp) REVERT: E 90 MET cc_start: 0.9417 (mmp) cc_final: 0.9125 (mmp) REVERT: G 64 GLU cc_start: 0.9815 (tt0) cc_final: 0.9462 (tm-30) REVERT: G 104 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9184 (mm-40) REVERT: H 62 MET cc_start: 0.9613 (mmp) cc_final: 0.9325 (mmp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3378 time to fit residues: 45.5660 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 : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3046 r_free = 0.3046 target = 0.034392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.023347 restraints weight = 262583.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.023741 restraints weight = 152899.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024120 restraints weight = 109600.216| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16745 Z= 0.230 Angle : 0.618 12.611 24116 Z= 0.359 Chirality : 0.038 0.318 2753 Planarity : 0.005 0.062 1880 Dihedral : 30.881 179.069 4954 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1100 helix: 1.61 (0.19), residues: 705 sheet: -1.36 (0.85), residues: 29 loop : -0.72 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 61 HIS 0.006 0.001 HIS L 65 PHE 0.009 0.001 PHE D 65 TYR 0.014 0.001 TYR F 72 ARG 0.005 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.06361 ( 896) hydrogen bonds : angle 3.66871 ( 2286) metal coordination : bond 0.00785 ( 8) metal coordination : angle 2.64119 ( 9) covalent geometry : bond 0.00502 (16737) covalent geometry : angle 0.61606 (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 93 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.342 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 74 ILE cc_start: 0.9745 (tp) cc_final: 0.9532 (tp) REVERT: A 90 MET cc_start: 0.9318 (mmp) cc_final: 0.9044 (mmp) REVERT: A 99 TYR cc_start: 0.9483 (t80) cc_final: 0.9227 (t80) REVERT: B 59 LYS cc_start: 0.9536 (tptm) cc_final: 0.9252 (tptp) REVERT: D 37 TYR cc_start: 0.9478 (m-10) cc_final: 0.9077 (m-10) REVERT: D 59 MET cc_start: 0.9129 (tpp) cc_final: 0.8863 (tpp) REVERT: D 102 LEU cc_start: 0.9465 (mt) cc_final: 0.9185 (tp) REVERT: E 90 MET cc_start: 0.9431 (mmp) cc_final: 0.9153 (mmm) REVERT: E 120 MET cc_start: 0.8467 (ptp) cc_final: 0.8075 (ptp) REVERT: G 61 GLU cc_start: 0.9541 (tp30) cc_final: 0.9203 (tp30) REVERT: G 64 GLU cc_start: 0.9808 (tt0) cc_final: 0.9402 (tm-30) REVERT: G 104 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9098 (mm-40) REVERT: H 62 MET cc_start: 0.9622 (mmp) cc_final: 0.9336 (mmp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3450 time to fit residues: 45.6730 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 : 1.316 ------------------------------------------------------------------------------- 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: 0.0970 chunk 86 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.023542 restraints weight = 259368.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023935 restraints weight = 150999.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024100 restraints weight = 110208.313| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16745 Z= 0.196 Angle : 0.614 13.606 24116 Z= 0.353 Chirality : 0.037 0.317 2753 Planarity : 0.004 0.062 1880 Dihedral : 30.884 179.193 4954 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.25), residues: 1100 helix: 1.58 (0.19), residues: 705 sheet: -1.30 (0.84), residues: 29 loop : -0.69 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 61 HIS 0.008 0.001 HIS L 65 PHE 0.013 0.001 PHE A 104 TYR 0.017 0.001 TYR L 64 ARG 0.005 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 896) hydrogen bonds : angle 3.61144 ( 2286) metal coordination : bond 0.00685 ( 8) metal coordination : angle 2.73006 ( 9) covalent geometry : bond 0.00424 (16737) covalent geometry : angle 0.61169 (24107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4773.92 seconds wall clock time: 84 minutes 17.09 seconds (5057.09 seconds total)