Starting phenix.real_space_refine on Fri Mar 15 21:13:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/03_2024/8txv_41706.pdb" } resolution = 3.8 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 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7144 2.51 5 N 2407 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "G ASP 72": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 7.38, per 1000 atoms: 0.57 Number of scatterers: 12836 At special positions: 0 Unit cell: (94.288, 124.832, 120.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 294 15.00 O 2976 8.00 N 2407 7.00 C 7144 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 - 3.50 Amino acid : False - 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: 5.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 66.7% alpha, 4.4% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.576A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.596A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.567A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.881A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.793A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.014A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.615A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.712A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.640A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.603A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.528A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.709A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 8.825A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2529 1.33 - 1.45: 4339 1.45 - 1.57: 6179 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13659 Sorted by residual: bond pdb=" CG1 ILE A 112 " pdb=" CD1 ILE A 112 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CB ASP C 72 " pdb=" CG ASP C 72 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB ASP E 81 " pdb=" CG ASP E 81 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.98e-01 ... (remaining 13654 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.45: 1342 105.45 - 112.22: 7541 112.22 - 118.98: 3419 118.98 - 125.74: 6401 125.74 - 132.51: 995 Bond angle restraints: 19698 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CB ARG B 67 " pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " ideal model delta sigma weight residual 111.30 118.48 -7.18 2.30e+00 1.89e-01 9.74e+00 angle pdb=" CA ARG B 67 " pdb=" CB ARG B 67 " pdb=" CG ARG B 67 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 angle pdb=" N GLN A 125 " pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " ideal model delta sigma weight residual 110.28 113.84 -3.56 1.55e+00 4.16e-01 5.28e+00 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 5858 29.37 - 58.74: 1526 58.74 - 88.12: 103 88.12 - 117.49: 2 117.49 - 146.86: 2 Dihedral angle restraints: 7491 sinusoidal: 5008 harmonic: 2483 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 73.14 146.86 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.89 144.11 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " pdb=" CD GLU C 56 " pdb=" OE1 GLU C 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1558 0.028 - 0.055: 471 0.055 - 0.083: 135 0.083 - 0.110: 62 0.110 - 0.138: 14 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2237 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.92e-03 2.19e+00 pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.021 2.00e-02 2.50e+03 8.33e-03 2.08e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.018 2.00e-02 2.50e+03 7.34e-03 1.61e+00 pdb=" N9 DG I 26 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1670 2.76 - 3.47: 17444 3.47 - 4.19: 34430 4.19 - 4.90: 52456 Nonbonded interactions: 106002 Sorted by model distance: nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.329 3.350 nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.151 2.496 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.219 2.440 nonbonded pdb=" O SER D 123 " pdb=" N SER C 11 " model vdw 2.246 2.520 ... (remaining 105997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.030 Check model and map are aligned: 0.190 Set scattering table: 0.090 Process input model: 40.830 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.003 0.049 13659 Z= 0.178 Angle : 0.557 7.178 19698 Z= 0.330 Chirality : 0.033 0.138 2240 Planarity : 0.003 0.038 1478 Dihedral : 26.649 146.860 5891 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.47 (0.30), residues: 839 helix: 2.61 (0.22), residues: 544 sheet: 1.56 (1.19), residues: 26 loop : -0.45 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.009 0.001 PHE E 78 TYR 0.020 0.001 TYR H 40 ARG 0.013 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (t70) REVERT: B 31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8770 (ttpp) REVERT: B 91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt) REVERT: D 51 ASP cc_start: 0.9279 (p0) cc_final: 0.8711 (p0) REVERT: D 116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt) REVERT: D 120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt) REVERT: E 57 SER cc_start: 0.9388 (p) cc_final: 0.8894 (p) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20) REVERT: E 82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm) REVERT: E 94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 110 CYS cc_start: 0.7931 (m) cc_final: 0.7656 (m) REVERT: E 129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8743 (tpt-90) REVERT: F 91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt) REVERT: H 59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp) REVERT: H 85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8923 (mttp) REVERT: M 44 ILE cc_start: 0.5531 (mm) cc_final: 0.4842 (mp) REVERT: C 64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30) REVERT: G 41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8178 (tm-30) REVERT: G 64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3062 time to fit residues: 93.5278 Evaluate side-chains 179 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 0.0040 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13659 Z= 0.181 Angle : 0.558 6.713 19698 Z= 0.330 Chirality : 0.034 0.153 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.492 147.476 4171 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 11.93 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.63 (0.29), residues: 839 helix: 2.75 (0.22), residues: 554 sheet: 1.09 (1.14), residues: 26 loop : -0.50 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.012 0.001 PHE A 78 TYR 0.011 0.001 TYR B 88 ARG 0.007 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8335 (m-30) cc_final: 0.7924 (t70) REVERT: A 125 GLN cc_start: 0.8136 (mt0) cc_final: 0.7603 (mp10) REVERT: A 129 ARG cc_start: 0.8862 (tpt90) cc_final: 0.8392 (tpt90) REVERT: B 31 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8834 (ttpp) REVERT: B 91 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9247 (ttmt) REVERT: D 51 ASP cc_start: 0.9302 (p0) cc_final: 0.8742 (p0) REVERT: D 85 LYS cc_start: 0.9277 (mttm) cc_final: 0.8988 (mmtt) REVERT: D 92 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8372 (ttm170) REVERT: D 120 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8842 (tttt) REVERT: E 57 SER cc_start: 0.9321 (p) cc_final: 0.8863 (p) REVERT: E 59 GLU cc_start: 0.8801 (pm20) cc_final: 0.7894 (pm20) REVERT: E 82 LEU cc_start: 0.9401 (mt) cc_final: 0.9141 (mm) REVERT: E 105 GLU cc_start: 0.8608 (tp30) cc_final: 0.8165 (tp30) REVERT: F 85 ASP cc_start: 0.8867 (m-30) cc_final: 0.8424 (m-30) REVERT: F 88 TYR cc_start: 0.8260 (m-10) cc_final: 0.8047 (m-10) REVERT: F 91 LYS cc_start: 0.9157 (tttp) cc_final: 0.8796 (ttmt) REVERT: H 83 TYR cc_start: 0.8586 (m-10) cc_final: 0.8338 (m-80) REVERT: H 85 LYS cc_start: 0.9306 (mttm) cc_final: 0.8804 (mtmm) REVERT: M 62 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: C 64 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8287 (tm-30) REVERT: G 41 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8143 (tm-30) REVERT: G 64 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8667 (tm-30) outliers start: 10 outliers final: 7 residues processed: 196 average time/residue: 0.3044 time to fit residues: 80.1349 Evaluate side-chains 184 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13659 Z= 0.423 Angle : 0.663 8.875 19698 Z= 0.381 Chirality : 0.039 0.148 2240 Planarity : 0.004 0.038 1478 Dihedral : 29.874 150.101 4171 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.88 % Allowed : 14.70 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.26 (0.29), residues: 839 helix: 2.47 (0.22), residues: 554 sheet: 2.17 (1.29), residues: 18 loop : -0.69 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.020 0.002 PHE A 78 TYR 0.031 0.002 TYR B 88 ARG 0.009 0.001 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8141 (m-30) cc_final: 0.7714 (t70) REVERT: A 123 ASP cc_start: 0.9438 (m-30) cc_final: 0.9216 (m-30) REVERT: B 88 TYR cc_start: 0.8569 (m-10) cc_final: 0.7861 (m-10) REVERT: B 91 LYS cc_start: 0.9517 (ttmm) cc_final: 0.9248 (ttmt) REVERT: D 42 TYR cc_start: 0.8689 (t80) cc_final: 0.8070 (t80) REVERT: D 46 LYS cc_start: 0.9378 (tppt) cc_final: 0.8964 (tppt) REVERT: D 51 ASP cc_start: 0.9343 (p0) cc_final: 0.8811 (p0) REVERT: D 83 TYR cc_start: 0.8268 (m-10) cc_final: 0.7417 (m-10) REVERT: D 85 LYS cc_start: 0.9357 (mttm) cc_final: 0.9105 (mmtt) REVERT: D 120 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8973 (ttmm) REVERT: E 57 SER cc_start: 0.9432 (p) cc_final: 0.8933 (p) REVERT: E 59 GLU cc_start: 0.8918 (pm20) cc_final: 0.7976 (pm20) REVERT: E 82 LEU cc_start: 0.9582 (mt) cc_final: 0.9337 (mm) REVERT: E 105 GLU cc_start: 0.8724 (tp30) cc_final: 0.8397 (tp30) REVERT: F 88 TYR cc_start: 0.8774 (m-10) cc_final: 0.8279 (m-10) REVERT: F 91 LYS cc_start: 0.9281 (tttp) cc_final: 0.8979 (ttmt) REVERT: H 85 LYS cc_start: 0.9308 (mttm) cc_final: 0.8789 (mtmm) REVERT: C 64 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 41 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 64 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8742 (tm-30) outliers start: 27 outliers final: 24 residues processed: 187 average time/residue: 0.2840 time to fit residues: 72.3986 Evaluate side-chains 189 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13659 Z= 0.196 Angle : 0.565 8.013 19698 Z= 0.332 Chirality : 0.034 0.151 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.610 147.954 4171 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.50 % Allowed : 17.34 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.58 (0.29), residues: 839 helix: 2.76 (0.22), residues: 554 sheet: 2.16 (1.26), residues: 18 loop : -0.67 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.016 0.001 PHE A 78 TYR 0.010 0.001 TYR B 88 ARG 0.007 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8230 (m-30) cc_final: 0.7878 (t70) REVERT: A 123 ASP cc_start: 0.9388 (m-30) cc_final: 0.9156 (m-30) REVERT: A 125 GLN cc_start: 0.8132 (mt0) cc_final: 0.7212 (mp10) REVERT: B 79 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8680 (mtmm) REVERT: B 88 TYR cc_start: 0.8459 (m-10) cc_final: 0.7860 (m-10) REVERT: B 91 LYS cc_start: 0.9504 (ttmm) cc_final: 0.9218 (ttmt) REVERT: D 51 ASP cc_start: 0.9300 (p0) cc_final: 0.8747 (p0) REVERT: D 83 TYR cc_start: 0.8139 (m-10) cc_final: 0.7495 (m-10) REVERT: D 85 LYS cc_start: 0.9344 (mttm) cc_final: 0.9123 (mmtt) REVERT: D 120 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8848 (tttt) REVERT: E 57 SER cc_start: 0.9399 (p) cc_final: 0.8932 (p) REVERT: E 59 GLU cc_start: 0.8848 (pm20) cc_final: 0.7933 (pm20) REVERT: E 82 LEU cc_start: 0.9508 (mt) cc_final: 0.9236 (mm) REVERT: F 88 TYR cc_start: 0.8708 (m-10) cc_final: 0.8265 (m-10) REVERT: F 91 LYS cc_start: 0.9240 (tttp) cc_final: 0.8949 (ttmt) REVERT: H 83 TYR cc_start: 0.8843 (m-10) cc_final: 0.8167 (m-80) REVERT: H 85 LYS cc_start: 0.9309 (mttm) cc_final: 0.8790 (mtmm) REVERT: C 64 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8432 (tm-30) REVERT: G 41 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8083 (tm-30) REVERT: G 64 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8661 (tm-30) outliers start: 17 outliers final: 14 residues processed: 187 average time/residue: 0.2827 time to fit residues: 73.7116 Evaluate side-chains 184 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13659 Z= 0.361 Angle : 0.630 8.477 19698 Z= 0.364 Chirality : 0.037 0.151 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.808 150.201 4171 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.88 % Allowed : 18.03 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.39 (0.29), residues: 839 helix: 2.59 (0.22), residues: 554 sheet: 2.26 (1.27), residues: 18 loop : -0.71 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE A 78 TYR 0.017 0.002 TYR B 88 ARG 0.008 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8126 (m-30) cc_final: 0.7850 (t70) REVERT: A 123 ASP cc_start: 0.9445 (m-30) cc_final: 0.9241 (m-30) REVERT: A 125 GLN cc_start: 0.8217 (mt0) cc_final: 0.7452 (mt0) REVERT: B 88 TYR cc_start: 0.8587 (m-10) cc_final: 0.7851 (m-10) REVERT: B 91 LYS cc_start: 0.9497 (ttmm) cc_final: 0.9209 (ttmt) REVERT: D 46 LYS cc_start: 0.9315 (tppt) cc_final: 0.9045 (mmtm) REVERT: D 51 ASP cc_start: 0.9354 (p0) cc_final: 0.8835 (p0) REVERT: D 83 TYR cc_start: 0.8340 (m-10) cc_final: 0.7557 (m-10) REVERT: D 85 LYS cc_start: 0.9369 (mttm) cc_final: 0.9152 (mmtt) REVERT: D 120 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8941 (ttmm) REVERT: E 57 SER cc_start: 0.9420 (p) cc_final: 0.8911 (p) REVERT: E 59 GLU cc_start: 0.8870 (pm20) cc_final: 0.7933 (pm20) REVERT: E 82 LEU cc_start: 0.9567 (mt) cc_final: 0.9323 (mm) REVERT: F 88 TYR cc_start: 0.8745 (m-10) cc_final: 0.8248 (m-10) REVERT: F 91 LYS cc_start: 0.9288 (tttp) cc_final: 0.9043 (ttmt) REVERT: H 85 LYS cc_start: 0.9304 (mttm) cc_final: 0.8796 (mtmm) REVERT: C 64 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8329 (tm-30) REVERT: G 41 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8123 (tm-30) REVERT: G 64 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8733 (tm-30) outliers start: 27 outliers final: 26 residues processed: 181 average time/residue: 0.2775 time to fit residues: 69.1300 Evaluate side-chains 192 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13659 Z= 0.203 Angle : 0.573 7.876 19698 Z= 0.336 Chirality : 0.034 0.155 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.656 148.606 4171 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.47 % Allowed : 18.03 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.56 (0.30), residues: 839 helix: 2.75 (0.22), residues: 555 sheet: 2.13 (1.25), residues: 18 loop : -0.72 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.012 0.001 PHE A 78 TYR 0.010 0.001 TYR C 50 ARG 0.008 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8109 (m-30) cc_final: 0.7875 (t70) REVERT: A 123 ASP cc_start: 0.9390 (m-30) cc_final: 0.9167 (m-30) REVERT: A 125 GLN cc_start: 0.8162 (mt0) cc_final: 0.7320 (mt0) REVERT: B 67 ARG cc_start: 0.7045 (mmp80) cc_final: 0.6708 (ttm110) REVERT: B 88 TYR cc_start: 0.8540 (m-10) cc_final: 0.7824 (m-10) REVERT: B 91 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9193 (ttmt) REVERT: D 46 LYS cc_start: 0.9255 (tppt) cc_final: 0.8996 (tppt) REVERT: D 51 ASP cc_start: 0.9320 (p0) cc_final: 0.8785 (p0) REVERT: D 83 TYR cc_start: 0.8216 (m-10) cc_final: 0.7441 (m-10) REVERT: D 85 LYS cc_start: 0.9365 (mttm) cc_final: 0.9143 (mmtt) REVERT: D 100 LEU cc_start: 0.9324 (mt) cc_final: 0.9087 (mt) REVERT: D 120 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8816 (tttt) REVERT: E 57 SER cc_start: 0.9395 (p) cc_final: 0.8900 (p) REVERT: E 59 GLU cc_start: 0.8866 (pm20) cc_final: 0.7949 (pm20) REVERT: E 82 LEU cc_start: 0.9522 (mt) cc_final: 0.9255 (mm) REVERT: F 88 TYR cc_start: 0.8704 (m-10) cc_final: 0.8480 (m-10) REVERT: F 91 LYS cc_start: 0.9299 (tttp) cc_final: 0.9062 (ttmt) REVERT: H 85 LYS cc_start: 0.9286 (mttm) cc_final: 0.8782 (mtmm) REVERT: C 64 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8449 (tm-30) REVERT: G 41 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8716 (tm-30) outliers start: 24 outliers final: 20 residues processed: 187 average time/residue: 0.2727 time to fit residues: 70.6929 Evaluate side-chains 190 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 13659 Z= 0.429 Angle : 0.669 8.801 19698 Z= 0.383 Chirality : 0.039 0.154 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.932 150.628 4171 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.44 % Allowed : 17.34 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.27 (0.29), residues: 839 helix: 2.50 (0.22), residues: 553 sheet: 2.16 (1.26), residues: 18 loop : -0.74 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 78 TYR 0.018 0.002 TYR B 88 ARG 0.012 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7708 (t80) cc_final: 0.7139 (t80) REVERT: A 81 ASP cc_start: 0.8208 (m-30) cc_final: 0.7916 (t70) REVERT: A 123 ASP cc_start: 0.9456 (m-30) cc_final: 0.9232 (m-30) REVERT: A 125 GLN cc_start: 0.8164 (mt0) cc_final: 0.7470 (mt0) REVERT: B 67 ARG cc_start: 0.7032 (mmp80) cc_final: 0.6587 (ttm110) REVERT: B 88 TYR cc_start: 0.8546 (m-10) cc_final: 0.8268 (m-10) REVERT: B 91 LYS cc_start: 0.9498 (ttmm) cc_final: 0.9231 (ttmt) REVERT: D 46 LYS cc_start: 0.9351 (tppt) cc_final: 0.9091 (tppt) REVERT: D 51 ASP cc_start: 0.9373 (p0) cc_final: 0.8850 (p0) REVERT: D 85 LYS cc_start: 0.9384 (mttm) cc_final: 0.9176 (mmtt) REVERT: D 100 LEU cc_start: 0.9289 (mt) cc_final: 0.9030 (mt) REVERT: D 120 LYS cc_start: 0.9207 (ttpt) cc_final: 0.8957 (ttmm) REVERT: E 57 SER cc_start: 0.9408 (p) cc_final: 0.8898 (p) REVERT: E 59 GLU cc_start: 0.8921 (pm20) cc_final: 0.8066 (pm20) REVERT: E 81 ASP cc_start: 0.8478 (t0) cc_final: 0.8253 (t0) REVERT: E 82 LEU cc_start: 0.9581 (mt) cc_final: 0.9330 (mm) REVERT: E 105 GLU cc_start: 0.8752 (tp30) cc_final: 0.8448 (tp30) REVERT: F 88 TYR cc_start: 0.8736 (m-10) cc_final: 0.8291 (m-10) REVERT: F 91 LYS cc_start: 0.9313 (tttp) cc_final: 0.9071 (ttmt) REVERT: H 85 LYS cc_start: 0.9312 (mttm) cc_final: 0.8803 (mtmm) REVERT: C 64 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 41 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 64 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8756 (tm-30) outliers start: 31 outliers final: 30 residues processed: 183 average time/residue: 0.2847 time to fit residues: 71.4288 Evaluate side-chains 200 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13659 Z= 0.205 Angle : 0.587 8.636 19698 Z= 0.341 Chirality : 0.034 0.150 2240 Planarity : 0.004 0.038 1478 Dihedral : 29.681 148.762 4171 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.33 % Allowed : 19.42 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.55 (0.29), residues: 839 helix: 2.73 (0.22), residues: 554 sheet: 2.20 (1.28), residues: 18 loop : -0.68 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.014 0.001 PHE A 78 TYR 0.010 0.001 TYR C 57 ARG 0.010 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7546 (t80) cc_final: 0.6987 (t80) REVERT: A 81 ASP cc_start: 0.8187 (m-30) cc_final: 0.7951 (t70) REVERT: A 123 ASP cc_start: 0.9400 (m-30) cc_final: 0.8855 (m-30) REVERT: A 125 GLN cc_start: 0.8153 (mt0) cc_final: 0.7363 (mt0) REVERT: B 67 ARG cc_start: 0.7250 (mmp80) cc_final: 0.6881 (ttm110) REVERT: B 88 TYR cc_start: 0.8481 (m-10) cc_final: 0.7758 (m-10) REVERT: B 91 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9225 (ttmt) REVERT: D 51 ASP cc_start: 0.9325 (p0) cc_final: 0.8800 (p0) REVERT: D 83 TYR cc_start: 0.8309 (m-10) cc_final: 0.7491 (m-10) REVERT: D 85 LYS cc_start: 0.9371 (mttm) cc_final: 0.9153 (mmtt) REVERT: D 120 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8886 (ttmm) REVERT: E 57 SER cc_start: 0.9341 (p) cc_final: 0.8894 (p) REVERT: E 59 GLU cc_start: 0.8868 (pm20) cc_final: 0.8043 (pm20) REVERT: E 82 LEU cc_start: 0.9521 (mt) cc_final: 0.9285 (mm) REVERT: E 105 GLU cc_start: 0.8691 (tp30) cc_final: 0.8347 (tp30) REVERT: F 88 TYR cc_start: 0.8687 (m-10) cc_final: 0.8474 (m-10) REVERT: F 91 LYS cc_start: 0.9273 (tttp) cc_final: 0.9040 (ttmt) REVERT: H 85 LYS cc_start: 0.9294 (mttm) cc_final: 0.8794 (mtmm) REVERT: C 64 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 92 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8459 (mt-10) REVERT: G 41 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8183 (tm-30) REVERT: G 64 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8678 (tm-30) outliers start: 23 outliers final: 19 residues processed: 185 average time/residue: 0.2754 time to fit residues: 70.3956 Evaluate side-chains 190 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13659 Z= 0.198 Angle : 0.584 11.127 19698 Z= 0.338 Chirality : 0.034 0.166 2240 Planarity : 0.003 0.038 1478 Dihedral : 29.611 148.933 4171 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.91 % Allowed : 20.25 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.60 (0.29), residues: 839 helix: 2.75 (0.22), residues: 556 sheet: 1.31 (1.11), residues: 26 loop : -0.63 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 109 PHE 0.012 0.001 PHE A 78 TYR 0.010 0.001 TYR D 42 ARG 0.010 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7597 (t80) cc_final: 0.7124 (t80) REVERT: A 81 ASP cc_start: 0.8166 (m-30) cc_final: 0.7950 (t70) REVERT: A 123 ASP cc_start: 0.9371 (m-30) cc_final: 0.9144 (m-30) REVERT: A 125 GLN cc_start: 0.8151 (mt0) cc_final: 0.7321 (mt0) REVERT: B 67 ARG cc_start: 0.7348 (mmp80) cc_final: 0.6842 (ttm-80) REVERT: B 88 TYR cc_start: 0.8472 (m-10) cc_final: 0.7814 (m-10) REVERT: B 91 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9239 (ttmt) REVERT: D 51 ASP cc_start: 0.9291 (p0) cc_final: 0.8738 (p0) REVERT: D 83 TYR cc_start: 0.8224 (m-10) cc_final: 0.7500 (m-10) REVERT: D 85 LYS cc_start: 0.9362 (mttm) cc_final: 0.9146 (mmtt) REVERT: D 120 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8861 (ttmm) REVERT: E 57 SER cc_start: 0.9311 (p) cc_final: 0.8863 (p) REVERT: E 59 GLU cc_start: 0.8836 (pm20) cc_final: 0.8015 (pm20) REVERT: E 82 LEU cc_start: 0.9496 (mt) cc_final: 0.9241 (mm) REVERT: E 105 GLU cc_start: 0.8690 (tp30) cc_final: 0.8383 (tp30) REVERT: F 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8416 (m-10) REVERT: F 91 LYS cc_start: 0.9268 (tttp) cc_final: 0.9046 (ttmt) REVERT: H 83 TYR cc_start: 0.8786 (m-10) cc_final: 0.7770 (m-80) REVERT: H 85 LYS cc_start: 0.9329 (mttm) cc_final: 0.8836 (mtmm) REVERT: C 64 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 92 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8448 (mt-10) REVERT: G 41 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 64 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8764 (tm-30) outliers start: 20 outliers final: 20 residues processed: 188 average time/residue: 0.2626 time to fit residues: 68.3673 Evaluate side-chains 191 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 40 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 13659 Z= 0.521 Angle : 0.735 10.164 19698 Z= 0.415 Chirality : 0.042 0.161 2240 Planarity : 0.005 0.039 1478 Dihedral : 30.055 151.605 4171 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.47 % Allowed : 19.42 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.09 (0.29), residues: 839 helix: 2.34 (0.22), residues: 555 sheet: 2.10 (1.26), residues: 18 loop : -0.79 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 49 PHE 0.016 0.002 PHE A 78 TYR 0.022 0.003 TYR A 99 ARG 0.009 0.001 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8221 (m-30) cc_final: 0.7911 (t70) REVERT: A 125 GLN cc_start: 0.8172 (mt0) cc_final: 0.7542 (mt0) REVERT: B 88 TYR cc_start: 0.8559 (m-10) cc_final: 0.8218 (m-10) REVERT: B 91 LYS cc_start: 0.9513 (ttmm) cc_final: 0.9285 (ttmt) REVERT: D 51 ASP cc_start: 0.9439 (p0) cc_final: 0.8955 (p0) REVERT: D 85 LYS cc_start: 0.9370 (mttm) cc_final: 0.9159 (mmtt) REVERT: D 120 LYS cc_start: 0.9217 (ttpt) cc_final: 0.8964 (ttmm) REVERT: E 57 SER cc_start: 0.9359 (p) cc_final: 0.8754 (p) REVERT: E 59 GLU cc_start: 0.8928 (pm20) cc_final: 0.8052 (pm20) REVERT: E 81 ASP cc_start: 0.8508 (t0) cc_final: 0.8272 (t0) REVERT: E 82 LEU cc_start: 0.9573 (mt) cc_final: 0.9333 (mm) REVERT: F 88 TYR cc_start: 0.8743 (m-10) cc_final: 0.8529 (m-10) REVERT: F 91 LYS cc_start: 0.9325 (tttp) cc_final: 0.9077 (ttmt) REVERT: H 85 LYS cc_start: 0.9319 (mttm) cc_final: 0.8799 (mtmm) REVERT: C 64 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8358 (tm-30) REVERT: G 41 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 64 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8778 (tm-30) outliers start: 24 outliers final: 20 residues processed: 178 average time/residue: 0.2884 time to fit residues: 70.4556 Evaluate side-chains 185 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.054846 restraints weight = 43856.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.056976 restraints weight = 20451.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.058320 restraints weight = 13331.330| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13659 Z= 0.216 Angle : 0.608 9.817 19698 Z= 0.351 Chirality : 0.035 0.143 2240 Planarity : 0.004 0.039 1478 Dihedral : 29.773 149.146 4171 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.77 % Allowed : 20.25 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.48 (0.29), residues: 839 helix: 2.67 (0.22), residues: 556 sheet: 1.18 (1.07), residues: 26 loop : -0.70 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 78 TYR 0.011 0.001 TYR D 40 ARG 0.007 0.000 ARG M 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.32 seconds wall clock time: 41 minutes 29.66 seconds (2489.66 seconds total)