Starting phenix.real_space_refine on Sun Mar 17 09:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/03_2024/8hqy_34954.pdb" } resolution = 3.05 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 5090 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: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 12 5.16 5 C 6888 2.51 5 N 2298 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "S ARG 167": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2775 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2801 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Time building chain proxies: 6.20, per 1000 atoms: 0.50 Number of scatterers: 12302 At special positions: 0 Unit cell: (123.51, 102.03, 115.992, 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 12 16.00 P 272 15.00 O 2832 8.00 N 2298 7.00 C 6888 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: 5.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 67.0% alpha, 4.2% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.984A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.667A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.665A 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 41 removed outlier: 3.605A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.718A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.534A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.683A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.676A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.533A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.124A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.684A 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 79 removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 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 77 removed outlier: 3.722A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.494A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.710A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.678A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.567A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.749A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 removed outlier: 3.529A pdb=" N LYS U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.783A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.569A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.528A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.786A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.495A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.566A pdb=" N LEU U 15 " --> pdb=" O ILE U 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 2020 1.32 - 1.44: 4361 1.44 - 1.56: 6123 1.56 - 1.68: 542 1.68 - 1.80: 23 Bond restraints: 13069 Sorted by residual: bond pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.86e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.39e+00 bond pdb=" C HIS H 49 " pdb=" N PRO H 50 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.48e+00 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.10e+00 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.20e+00 ... (remaining 13064 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.26: 1074 104.26 - 111.71: 6750 111.71 - 119.16: 4423 119.16 - 126.61: 5781 126.61 - 134.06: 785 Bond angle restraints: 18813 Sorted by residual: angle pdb=" N ARG U 72 " pdb=" CA ARG U 72 " pdb=" C ARG U 72 " ideal model delta sigma weight residual 110.91 116.07 -5.16 1.17e+00 7.31e-01 1.94e+01 angle pdb=" C SER S 181 " pdb=" N ASP S 182 " pdb=" CA ASP S 182 " ideal model delta sigma weight residual 121.80 132.51 -10.71 2.44e+00 1.68e-01 1.93e+01 angle pdb=" N ILE U 23 " pdb=" CA ILE U 23 " pdb=" C ILE U 23 " ideal model delta sigma weight residual 112.96 108.79 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" C LEU U 69 " pdb=" N VAL U 70 " pdb=" CA VAL U 70 " ideal model delta sigma weight residual 121.97 114.98 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" N ASP S 182 " pdb=" CA ASP S 182 " pdb=" C ASP S 182 " ideal model delta sigma weight residual 109.81 118.16 -8.35 2.21e+00 2.05e-01 1.43e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 5473 28.96 - 57.93: 1574 57.93 - 86.89: 119 86.89 - 115.85: 1 115.85 - 144.82: 3 Dihedral angle restraints: 7170 sinusoidal: 4714 harmonic: 2456 Sorted by residual: dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU U 71 " pdb=" C LEU U 71 " pdb=" N ARG U 72 " pdb=" CA ARG U 72 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA VAL U 70 " pdb=" C VAL U 70 " pdb=" N LEU U 71 " pdb=" CA LEU U 71 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1548 0.061 - 0.122: 511 0.122 - 0.183: 79 0.183 - 0.244: 10 0.244 - 0.306: 1 Chirality restraints: 2149 Sorted by residual: chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP S 182 " pdb=" N ASP S 182 " pdb=" C ASP S 182 " pdb=" CB ASP S 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2146 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.021 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE G 25 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.018 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE C 25 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 113 " -0.015 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG HIS A 113 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 113 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 113 " -0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2351 2.77 - 3.30: 10282 3.30 - 3.84: 24690 3.84 - 4.37: 28483 4.37 - 4.90: 40595 Nonbonded interactions: 106401 Sorted by model distance: nonbonded pdb=" O2 DC I 116 " pdb=" N2 DG J 32 " model vdw 2.238 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.264 2.440 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.274 2.496 nonbonded pdb=" O HIS D 109 " pdb=" OG SER D 112 " model vdw 2.288 2.440 nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.291 2.520 ... (remaining 106396 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' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 individual isotropic 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.100 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.011 0.113 13069 Z= 0.668 Angle : 1.013 11.952 18813 Z= 0.579 Chirality : 0.059 0.306 2149 Planarity : 0.007 0.052 1438 Dihedral : 27.346 144.817 5584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -3.02 (0.24), residues: 828 helix: -1.68 (0.18), residues: 551 sheet: -3.05 (0.99), residues: 20 loop : -2.24 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.020 0.004 HIS A 113 PHE 0.040 0.005 PHE C 25 TYR 0.021 0.003 TYR F 98 ARG 0.017 0.002 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 0.960 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: B 59 LYS cc_start: 0.9107 (tptt) cc_final: 0.8691 (tptp) REVERT: B 88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8138 (m-10) REVERT: C 104 GLN cc_start: 0.8399 (mm110) cc_final: 0.8064 (mm-40) REVERT: D 105 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7819 (tp30) REVERT: E 41 TYR cc_start: 0.8368 (m-80) cc_final: 0.8007 (m-10) REVERT: F 59 LYS cc_start: 0.9203 (tptm) cc_final: 0.8663 (mmmm) REVERT: F 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8478 (m-80) REVERT: G 15 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8382 (tmmt) REVERT: G 112 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8856 (mm110) REVERT: H 59 MET cc_start: 0.8941 (tpp) cc_final: 0.8616 (tpp) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7991 (m-10) REVERT: U 48 LYS cc_start: 0.8553 (pttt) cc_final: 0.8178 (pttp) REVERT: U 50 LEU cc_start: 0.7793 (mm) cc_final: 0.7516 (mm) REVERT: U 63 LYS cc_start: 0.7992 (mttt) cc_final: 0.7710 (mtpp) REVERT: U 68 HIS cc_start: 0.8526 (m-70) cc_final: 0.8247 (m90) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.3408 time to fit residues: 134.3479 Evaluate side-chains 218 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 GLN U 68 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13069 Z= 0.286 Angle : 0.667 10.650 18813 Z= 0.391 Chirality : 0.039 0.232 2149 Planarity : 0.005 0.043 1438 Dihedral : 31.008 148.157 3909 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.96 % Allowed : 11.85 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -0.46 (0.29), residues: 828 helix: 0.47 (0.21), residues: 553 sheet: -2.38 (1.00), residues: 20 loop : -1.77 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.005 0.001 HIS B 75 PHE 0.015 0.002 PHE E 67 TYR 0.032 0.002 TYR D 83 ARG 0.007 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8655 (mt-10) REVERT: A 59 GLU cc_start: 0.8589 (pm20) cc_final: 0.8344 (pm20) REVERT: A 106 ASP cc_start: 0.8052 (m-30) cc_final: 0.7646 (m-30) REVERT: B 59 LYS cc_start: 0.8958 (tptt) cc_final: 0.8723 (tptp) REVERT: B 63 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7941 (mt-10) REVERT: C 57 TYR cc_start: 0.9315 (t80) cc_final: 0.9005 (t80) REVERT: C 92 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7367 (mt-10) REVERT: D 63 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8649 (m-40) REVERT: D 108 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8623 (mtmt) REVERT: E 41 TYR cc_start: 0.8272 (m-80) cc_final: 0.8063 (m-10) REVERT: E 93 GLN cc_start: 0.8831 (tp40) cc_final: 0.8229 (tp40) REVERT: E 120 MET cc_start: 0.8353 (mmm) cc_final: 0.8134 (mmm) REVERT: F 25 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: F 59 LYS cc_start: 0.9267 (tptm) cc_final: 0.9052 (tptt) REVERT: G 15 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8357 (tmmt) REVERT: G 38 ASN cc_start: 0.8622 (m-40) cc_final: 0.8400 (m-40) REVERT: G 92 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 112 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8793 (mm110) REVERT: H 59 MET cc_start: 0.9078 (tpp) cc_final: 0.8790 (tpp) REVERT: H 79 ARG cc_start: 0.8844 (mtm-85) cc_final: 0.8624 (mtm110) REVERT: H 83 TYR cc_start: 0.8282 (m-10) cc_final: 0.7931 (m-10) REVERT: H 93 GLU cc_start: 0.8203 (mp0) cc_final: 0.7737 (mp0) REVERT: S 167 ARG cc_start: 0.8412 (mtp180) cc_final: 0.8054 (mtm-85) REVERT: U 13 ILE cc_start: 0.9145 (mm) cc_final: 0.8745 (mm) REVERT: U 15 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8040 (pp) REVERT: U 29 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8665 (mptt) REVERT: U 34 GLU cc_start: 0.8226 (pt0) cc_final: 0.8025 (pt0) REVERT: U 48 LYS cc_start: 0.8524 (pttt) cc_final: 0.8132 (pttp) outliers start: 21 outliers final: 12 residues processed: 264 average time/residue: 0.2727 time to fit residues: 98.9286 Evaluate side-chains 249 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13069 Z= 0.353 Angle : 0.664 7.143 18813 Z= 0.389 Chirality : 0.040 0.203 2149 Planarity : 0.005 0.047 1438 Dihedral : 30.800 149.890 3908 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.65 % Allowed : 13.54 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 0.52 (0.30), residues: 828 helix: 1.32 (0.22), residues: 552 sheet: -2.23 (1.02), residues: 19 loop : -1.60 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 164 HIS 0.007 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.022 0.002 TYR D 83 ARG 0.005 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.006 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: A 50 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 44 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8955 (mtpp) REVERT: B 59 LYS cc_start: 0.8979 (tptt) cc_final: 0.8600 (tptp) REVERT: B 63 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 57 TYR cc_start: 0.9370 (t80) cc_final: 0.9039 (t80) REVERT: D 51 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8357 (p0) REVERT: D 63 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (m110) REVERT: D 108 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8789 (mtmt) REVERT: E 41 TYR cc_start: 0.8236 (m-80) cc_final: 0.8030 (m-10) REVERT: E 93 GLN cc_start: 0.8963 (tp40) cc_final: 0.8534 (tp40) REVERT: G 15 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8334 (tmmt) REVERT: G 112 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8826 (mm110) REVERT: H 79 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8633 (mtm110) REVERT: H 83 TYR cc_start: 0.8339 (m-10) cc_final: 0.8116 (m-10) REVERT: H 93 GLU cc_start: 0.8206 (mp0) cc_final: 0.7651 (mp0) REVERT: U 13 ILE cc_start: 0.9081 (mm) cc_final: 0.8790 (mm) REVERT: U 15 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8198 (pp) REVERT: U 29 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8674 (mptt) REVERT: U 34 GLU cc_start: 0.8260 (pt0) cc_final: 0.8028 (pt0) outliers start: 33 outliers final: 18 residues processed: 243 average time/residue: 0.2785 time to fit residues: 92.1716 Evaluate side-chains 246 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 225 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13069 Z= 0.191 Angle : 0.591 7.430 18813 Z= 0.352 Chirality : 0.036 0.174 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.277 148.451 3908 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.95 % Allowed : 15.80 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 (0.30), residues: 828 helix: 1.96 (0.22), residues: 550 sheet: -1.97 (1.05), residues: 19 loop : -1.43 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.002 0.001 HIS A 113 PHE 0.012 0.001 PHE E 67 TYR 0.011 0.001 TYR D 83 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8602 (mt-10) REVERT: A 62 ILE cc_start: 0.9320 (mp) cc_final: 0.8058 (mp) REVERT: A 68 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: A 73 GLU cc_start: 0.8245 (tt0) cc_final: 0.7978 (tt0) REVERT: A 79 LYS cc_start: 0.8582 (tptp) cc_final: 0.8266 (tptt) REVERT: A 106 ASP cc_start: 0.8115 (m-30) cc_final: 0.7710 (m-30) REVERT: B 44 LYS cc_start: 0.9189 (mtpt) cc_final: 0.8974 (mtpp) REVERT: B 59 LYS cc_start: 0.8984 (tptt) cc_final: 0.8677 (tptp) REVERT: B 63 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7949 (mt-10) REVERT: C 57 TYR cc_start: 0.9272 (t80) cc_final: 0.8968 (t80) REVERT: C 64 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8404 (tm-30) REVERT: C 94 ASN cc_start: 0.9396 (t0) cc_final: 0.9101 (t0) REVERT: D 68 ASP cc_start: 0.8731 (t70) cc_final: 0.8404 (t0) REVERT: E 41 TYR cc_start: 0.8257 (m-80) cc_final: 0.8033 (m-10) REVERT: E 93 GLN cc_start: 0.8763 (tp40) cc_final: 0.8322 (tp40) REVERT: F 25 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8643 (t0) REVERT: F 88 TYR cc_start: 0.8873 (m-10) cc_final: 0.8225 (m-10) REVERT: G 15 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8329 (tmmt) REVERT: H 71 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7940 (tp30) REVERT: H 93 GLU cc_start: 0.8214 (mp0) cc_final: 0.7691 (mp0) REVERT: U 13 ILE cc_start: 0.9047 (mm) cc_final: 0.8360 (mm) REVERT: U 15 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8247 (pp) REVERT: U 29 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8661 (mptt) REVERT: U 69 LEU cc_start: 0.9147 (mp) cc_final: 0.8922 (mp) outliers start: 28 outliers final: 12 residues processed: 266 average time/residue: 0.2764 time to fit residues: 100.1643 Evaluate side-chains 247 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 58 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 89 ASN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN U 60 ASN U 68 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13069 Z= 0.312 Angle : 0.636 6.945 18813 Z= 0.371 Chirality : 0.038 0.180 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.443 149.031 3908 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.81 % Allowed : 17.35 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 828 helix: 2.09 (0.22), residues: 553 sheet: -2.05 (1.06), residues: 19 loop : -1.30 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.004 0.001 HIS A 113 PHE 0.012 0.002 PHE D 65 TYR 0.018 0.002 TYR H 83 ARG 0.013 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 68 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: A 79 LYS cc_start: 0.8563 (tptp) cc_final: 0.8270 (tptt) REVERT: A 81 ASP cc_start: 0.8801 (p0) cc_final: 0.8509 (p0) REVERT: A 106 ASP cc_start: 0.8002 (m-30) cc_final: 0.7750 (m-30) REVERT: B 44 LYS cc_start: 0.9320 (mtpt) cc_final: 0.9046 (mtpp) REVERT: B 59 LYS cc_start: 0.9035 (tptt) cc_final: 0.8639 (tptp) REVERT: B 63 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 57 TYR cc_start: 0.9358 (t80) cc_final: 0.9103 (t80) REVERT: C 64 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 92 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 94 ASN cc_start: 0.9427 (t0) cc_final: 0.9206 (t0) REVERT: D 68 ASP cc_start: 0.8798 (t70) cc_final: 0.8432 (t0) REVERT: D 116 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9049 (ttpp) REVERT: E 41 TYR cc_start: 0.8310 (m-80) cc_final: 0.8107 (m-10) REVERT: F 88 TYR cc_start: 0.8911 (m-10) cc_final: 0.8286 (m-80) REVERT: G 15 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8326 (tmmt) REVERT: H 71 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7960 (tp30) REVERT: H 83 TYR cc_start: 0.8194 (m-10) cc_final: 0.7940 (m-10) REVERT: U 6 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8970 (mmtp) REVERT: U 15 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8254 (pp) REVERT: U 29 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8725 (mptt) outliers start: 27 outliers final: 15 residues processed: 248 average time/residue: 0.2782 time to fit residues: 94.1919 Evaluate side-chains 248 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13069 Z= 0.228 Angle : 0.601 7.314 18813 Z= 0.354 Chirality : 0.036 0.169 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.288 147.828 3908 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.53 % Allowed : 18.19 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.79 (0.31), residues: 828 helix: 2.34 (0.22), residues: 552 sheet: -1.82 (1.01), residues: 19 loop : -1.24 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.014 0.001 PHE D 65 TYR 0.012 0.001 TYR H 83 ARG 0.009 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 243 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 68 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: A 79 LYS cc_start: 0.8569 (tptp) cc_final: 0.8276 (tptt) REVERT: A 81 ASP cc_start: 0.8776 (p0) cc_final: 0.8535 (p0) REVERT: A 106 ASP cc_start: 0.8004 (m-30) cc_final: 0.7773 (m-30) REVERT: B 44 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9011 (mtpp) REVERT: B 59 LYS cc_start: 0.9033 (tptt) cc_final: 0.8496 (tptp) REVERT: B 63 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 64 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 94 ASN cc_start: 0.9406 (t0) cc_final: 0.9183 (t0) REVERT: D 46 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8862 (mmmt) REVERT: D 68 ASP cc_start: 0.8757 (t70) cc_final: 0.8445 (t0) REVERT: D 116 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9065 (ttpp) REVERT: E 41 TYR cc_start: 0.8293 (m-80) cc_final: 0.8022 (m-10) REVERT: F 25 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8644 (t0) REVERT: G 15 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8320 (tmmt) REVERT: G 56 GLU cc_start: 0.8252 (tt0) cc_final: 0.7843 (mt-10) REVERT: H 71 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7949 (tp30) REVERT: H 83 TYR cc_start: 0.8139 (m-10) cc_final: 0.7879 (m-10) REVERT: U 15 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8043 (pp) REVERT: U 29 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8714 (mptt) outliers start: 25 outliers final: 10 residues processed: 253 average time/residue: 0.2680 time to fit residues: 92.1551 Evaluate side-chains 245 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 231 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 58 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13069 Z= 0.224 Angle : 0.601 6.989 18813 Z= 0.353 Chirality : 0.036 0.163 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.278 147.351 3908 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.82 % Allowed : 19.89 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.91 (0.31), residues: 828 helix: 2.42 (0.22), residues: 552 sheet: -2.00 (0.97), residues: 19 loop : -1.14 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.017 0.001 PHE D 65 TYR 0.021 0.001 TYR C 57 ARG 0.007 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8602 (mt-10) REVERT: A 68 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: A 79 LYS cc_start: 0.8564 (tptp) cc_final: 0.8269 (tptt) REVERT: A 81 ASP cc_start: 0.8767 (p0) cc_final: 0.8470 (p0) REVERT: B 59 LYS cc_start: 0.9027 (tptt) cc_final: 0.8683 (tptp) REVERT: B 63 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 92 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7515 (mt-10) REVERT: C 94 ASN cc_start: 0.9403 (t0) cc_final: 0.9171 (t0) REVERT: D 68 ASP cc_start: 0.8777 (t70) cc_final: 0.8458 (t0) REVERT: D 116 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (ttpp) REVERT: E 41 TYR cc_start: 0.8288 (m-80) cc_final: 0.8015 (m-10) REVERT: F 25 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8647 (t0) REVERT: F 88 TYR cc_start: 0.8882 (m-10) cc_final: 0.7864 (m-10) REVERT: G 15 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8328 (tmmt) REVERT: G 56 GLU cc_start: 0.8265 (tt0) cc_final: 0.7847 (mt-10) REVERT: G 89 ASN cc_start: 0.8989 (m110) cc_final: 0.8367 (m110) REVERT: H 71 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7965 (tp30) REVERT: U 15 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8052 (pp) REVERT: U 29 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8758 (mptt) REVERT: U 48 LYS cc_start: 0.8491 (pttt) cc_final: 0.7671 (ptmm) outliers start: 20 outliers final: 14 residues processed: 244 average time/residue: 0.2814 time to fit residues: 92.7799 Evaluate side-chains 248 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 58 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13069 Z= 0.202 Angle : 0.605 7.135 18813 Z= 0.354 Chirality : 0.035 0.159 2149 Planarity : 0.004 0.046 1438 Dihedral : 30.220 146.638 3908 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.40 % Allowed : 20.73 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.94 (0.31), residues: 828 helix: 2.47 (0.22), residues: 552 sheet: -2.55 (0.89), residues: 18 loop : -1.15 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.018 0.001 PHE D 65 TYR 0.050 0.002 TYR H 83 ARG 0.009 0.000 ARG S 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 68 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: A 79 LYS cc_start: 0.8566 (tptp) cc_final: 0.8278 (tptt) REVERT: A 81 ASP cc_start: 0.8753 (p0) cc_final: 0.8456 (p0) REVERT: B 44 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8712 (mtpt) REVERT: B 59 LYS cc_start: 0.9018 (tptt) cc_final: 0.8672 (tptp) REVERT: B 63 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 64 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8338 (tm-30) REVERT: C 92 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 94 ASN cc_start: 0.9392 (t0) cc_final: 0.9175 (t0) REVERT: D 46 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8841 (mmmt) REVERT: D 68 ASP cc_start: 0.8759 (t70) cc_final: 0.8427 (t0) REVERT: E 41 TYR cc_start: 0.8268 (m-80) cc_final: 0.8007 (m-10) REVERT: F 25 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8646 (t0) REVERT: F 88 TYR cc_start: 0.8694 (m-10) cc_final: 0.8019 (m-10) REVERT: G 15 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8320 (tmmt) REVERT: G 39 TYR cc_start: 0.9049 (m-80) cc_final: 0.8645 (m-80) REVERT: G 56 GLU cc_start: 0.8247 (tt0) cc_final: 0.7832 (mt-10) REVERT: G 89 ASN cc_start: 0.8995 (m110) cc_final: 0.8410 (m110) REVERT: H 71 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7924 (tp30) REVERT: H 83 TYR cc_start: 0.7954 (m-10) cc_final: 0.7578 (m-80) REVERT: H 93 GLU cc_start: 0.8280 (mp0) cc_final: 0.7876 (mp0) REVERT: S 164 TRP cc_start: 0.8425 (m100) cc_final: 0.8002 (m100) REVERT: U 15 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8001 (pp) REVERT: U 29 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8695 (mptt) REVERT: U 48 LYS cc_start: 0.8440 (pttt) cc_final: 0.7554 (ptmm) REVERT: U 64 GLU cc_start: 0.7120 (mp0) cc_final: 0.6625 (pm20) outliers start: 17 outliers final: 11 residues processed: 249 average time/residue: 0.2662 time to fit residues: 90.2288 Evaluate side-chains 248 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 58 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13069 Z= 0.405 Angle : 0.695 7.352 18813 Z= 0.397 Chirality : 0.041 0.193 2149 Planarity : 0.005 0.054 1438 Dihedral : 30.625 147.148 3908 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.24 % Allowed : 20.03 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.60 (0.31), residues: 828 helix: 2.19 (0.22), residues: 552 sheet: -2.69 (0.82), residues: 19 loop : -1.21 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP S 164 HIS 0.004 0.001 HIS D 49 PHE 0.014 0.002 PHE D 65 TYR 0.054 0.002 TYR H 83 ARG 0.007 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 68 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: A 79 LYS cc_start: 0.8603 (tptp) cc_final: 0.8267 (tptt) REVERT: A 81 ASP cc_start: 0.8786 (p0) cc_final: 0.8485 (p0) REVERT: B 44 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8806 (mtpt) REVERT: B 59 LYS cc_start: 0.9084 (tptt) cc_final: 0.8699 (tptp) REVERT: B 63 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 64 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 92 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7414 (mt-10) REVERT: D 68 ASP cc_start: 0.8855 (t70) cc_final: 0.8523 (t0) REVERT: F 25 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8729 (t0) REVERT: F 88 TYR cc_start: 0.8903 (m-10) cc_final: 0.8065 (m-10) REVERT: G 15 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8312 (tmmt) REVERT: H 71 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7897 (tp30) REVERT: U 29 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8695 (mptt) REVERT: U 64 GLU cc_start: 0.7350 (mp0) cc_final: 0.6729 (pm20) outliers start: 23 outliers final: 13 residues processed: 234 average time/residue: 0.2790 time to fit residues: 88.8042 Evaluate side-chains 234 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13069 Z= 0.287 Angle : 0.657 7.425 18813 Z= 0.379 Chirality : 0.038 0.192 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.448 146.275 3908 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.40 % Allowed : 21.02 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.67 (0.31), residues: 828 helix: 2.24 (0.22), residues: 553 sheet: -3.00 (0.73), residues: 18 loop : -1.19 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.001 PHE D 65 TYR 0.068 0.002 TYR H 83 ARG 0.005 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8600 (mt-10) REVERT: A 68 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: A 79 LYS cc_start: 0.8577 (tptp) cc_final: 0.8204 (tptt) REVERT: A 81 ASP cc_start: 0.8749 (p0) cc_final: 0.8404 (p0) REVERT: B 59 LYS cc_start: 0.9093 (tptt) cc_final: 0.8643 (tptp) REVERT: B 63 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 64 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 92 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 94 ASN cc_start: 0.9423 (t0) cc_final: 0.9191 (t0) REVERT: D 68 ASP cc_start: 0.8802 (t70) cc_final: 0.8456 (t0) REVERT: F 25 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8659 (t0) REVERT: G 15 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8374 (tmmt) REVERT: U 64 GLU cc_start: 0.7350 (mp0) cc_final: 0.6688 (pm20) outliers start: 17 outliers final: 14 residues processed: 237 average time/residue: 0.2753 time to fit residues: 88.8816 Evaluate side-chains 237 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3489 r_free = 0.3489 target = 0.060615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039759 restraints weight = 53669.996| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.43 r_work: 0.2631 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13069 Z= 0.209 Angle : 0.631 7.397 18813 Z= 0.364 Chirality : 0.036 0.166 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.231 145.666 3908 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.12 % Allowed : 21.30 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.75 (0.31), residues: 828 helix: 2.30 (0.22), residues: 553 sheet: -2.61 (0.76), residues: 18 loop : -1.16 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.001 PHE D 65 TYR 0.053 0.002 TYR H 83 ARG 0.005 0.000 ARG S 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.37 seconds wall clock time: 49 minutes 0.10 seconds (2940.10 seconds total)