Starting phenix.real_space_refine on Mon Apr 8 19:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/04_2024/6px3_20517.pdb" } resolution = 4.1 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= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 8074 2.51 5 N 2663 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "C GLU -56": "OE1" <-> "OE2" Residue "C GLU -8": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14323 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1393 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1819 Unusual residues: {' ZN': 3} Classifications: {'peptide': 233, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223, None: 3} Not linked: pdbres="THR S 325 " pdbres=" ZN S1001 " Not linked: pdbres=" ZN S1001 " pdbres=" ZN S1002 " Not linked: pdbres=" ZN S1002 " pdbres=" ZN S1003 " Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12981 SG CYS S 158 59.132 83.833 47.890 1.00358.91 S ATOM 13014 SG CYS S 163 61.737 82.243 50.744 1.00359.20 S ATOM 13051 SG CYS S 169 61.811 82.426 46.323 1.00377.57 S ATOM 12758 SG CYS S 129 58.755 80.167 51.153 1.00321.15 S ATOM 12772 SG CYS S 131 58.781 77.155 49.607 1.00322.61 S ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12910 SG CYS S 149 58.173 78.238 47.291 1.00299.48 S ATOM 13819 SG CYS S 261 37.845 88.685 19.012 1.00396.58 S ATOM 14198 SG CYS S 308 40.086 91.078 16.518 1.00413.35 S ATOM 14216 SG CYS S 310 40.442 89.010 15.411 1.00394.48 S ATOM 14250 SG CYS S 315 37.517 90.048 15.112 1.00394.57 S Time building chain proxies: 7.96, per 1000 atoms: 0.56 Number of scatterers: 14323 At special positions: 0 Unit cell: (93.6, 145.6, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 290 15.00 O 3260 8.00 N 2663 7.00 C 8074 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: 7.52 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.8% alpha, 7.1% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid -50 through -37 Processing helix chain 'C' and resid -35 through -33 No H-bonds generated for 'chain 'C' and resid -35 through -33' Processing helix chain 'C' and resid -17 through -12 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.632A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A 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 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.547A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.600A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.827A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid -60 through -56 removed outlier: 8.790A pdb=" N LEU C -5 " --> pdb=" O GLN C -70 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C -68 " --> pdb=" O LEU C -5 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C -3 " --> pdb=" O PHE C -68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C -66 " --> pdb=" O LEU C -3 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU C -1 " --> pdb=" O LYS C -66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB5, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.714A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 212 through 214 466 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2342 1.33 - 1.45: 5126 1.45 - 1.57: 7067 1.57 - 1.69: 578 1.69 - 1.81: 48 Bond restraints: 15161 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.29e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.47e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.501 -0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.43: 1428 105.43 - 112.88: 8338 112.88 - 120.33: 6273 120.33 - 127.78: 5216 127.78 - 135.23: 447 Bond angle restraints: 21702 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.41 -7.03 1.05e+00 9.07e-01 4.48e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.25 -7.25 1.10e+00 8.26e-01 4.34e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.12e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.58 4.47 1.09e+00 8.42e-01 1.68e+01 ... (remaining 21697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 6839 34.59 - 69.19: 1517 69.19 - 103.78: 17 103.78 - 138.38: 0 138.38 - 172.97: 4 Dihedral angle restraints: 8377 sinusoidal: 5318 harmonic: 3059 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.03 172.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1769 0.057 - 0.113: 550 0.113 - 0.170: 98 0.170 - 0.227: 25 0.227 - 0.283: 5 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO S 88 " pdb=" N PRO S 88 " pdb=" C PRO S 88 " pdb=" CB PRO S 88 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2444 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.60e-02 7.71e+00 pdb=" N9 DG J 106 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 2 1.67 - 2.48: 35 2.48 - 3.28: 14016 3.28 - 4.09: 41685 4.09 - 4.90: 65863 Warning: very small nonbonded interaction distances. Nonbonded interactions: 121601 Sorted by model distance: nonbonded pdb=" O GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 0.861 3.040 nonbonded pdb=" O GLN C -23 " pdb=" CD GLU D 102 " model vdw 1.590 3.270 nonbonded pdb=" O GLY C -25 " pdb=" OD1 ASP C 90 " model vdw 1.742 3.040 nonbonded pdb=" C GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 1.788 3.270 nonbonded pdb=" NE2 GLN C -23 " pdb=" CE1 HIS D 106 " model vdw 2.014 3.340 ... (remaining 121596 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' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'D' and resid 27 through 120) 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=0.89 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: 0.690 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: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 48.960 Find NCS groups from input model: 0.470 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.008 0.079 15161 Z= 0.410 Angle : 0.941 10.225 21702 Z= 0.573 Chirality : 0.057 0.283 2447 Planarity : 0.007 0.056 1760 Dihedral : 26.725 172.971 6407 Min Nonbonded Distance : 0.861 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % 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: -0.93 (0.23), residues: 1033 helix: 0.14 (0.19), residues: 564 sheet: -1.34 (0.57), residues: 71 loop : -1.49 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 135 HIS 0.005 0.001 HIS C -4 PHE 0.024 0.003 PHE B 61 TYR 0.017 0.003 TYR H 118 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9681 (m) cc_final: 0.9394 (p) REVERT: A 68 GLN cc_start: 0.9771 (tt0) cc_final: 0.9237 (tp-100) REVERT: A 80 THR cc_start: 0.9356 (m) cc_final: 0.8912 (p) REVERT: A 81 ASP cc_start: 0.8742 (t0) cc_final: 0.8414 (t0) REVERT: A 94 GLU cc_start: 0.8893 (tp30) cc_final: 0.8002 (tm-30) REVERT: A 105 GLU cc_start: 0.9274 (tp30) cc_final: 0.8923 (tm-30) REVERT: B 44 LYS cc_start: 0.9444 (tttt) cc_final: 0.9184 (ttpt) REVERT: B 49 LEU cc_start: 0.9752 (mt) cc_final: 0.9216 (mm) REVERT: B 59 LYS cc_start: 0.9615 (ttpt) cc_final: 0.9218 (tppp) REVERT: B 70 VAL cc_start: 0.9699 (t) cc_final: 0.9339 (p) REVERT: B 74 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8726 (pt0) REVERT: B 81 VAL cc_start: 0.9671 (t) cc_final: 0.9470 (p) REVERT: B 84 MET cc_start: 0.9403 (mmt) cc_final: 0.8448 (mmp) REVERT: B 88 TYR cc_start: 0.9481 (m-10) cc_final: 0.9241 (m-80) REVERT: B 97 LEU cc_start: 0.9271 (tp) cc_final: 0.8359 (tp) REVERT: C 25 PHE cc_start: 0.7986 (m-10) cc_final: 0.7643 (m-10) REVERT: C 39 TYR cc_start: 0.8910 (m-80) cc_final: 0.8172 (m-80) REVERT: C 56 GLU cc_start: 0.9195 (pp20) cc_final: 0.8499 (tt0) REVERT: C 68 ASN cc_start: 0.8857 (m-40) cc_final: 0.8646 (m110) REVERT: C 83 LEU cc_start: 0.9756 (mt) cc_final: 0.9489 (mt) REVERT: C 91 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9005 (mp0) REVERT: C 93 LEU cc_start: 0.9648 (mt) cc_final: 0.9343 (mt) REVERT: C 110 ASN cc_start: 0.9400 (t0) cc_final: 0.9029 (m110) REVERT: C 111 ILE cc_start: 0.9305 (mt) cc_final: 0.9084 (mm) REVERT: D 34 TYR cc_start: 0.9077 (m-80) cc_final: 0.8831 (m-80) REVERT: D 40 LYS cc_start: 0.9527 (mttt) cc_final: 0.9110 (mtmm) REVERT: D 64 ASN cc_start: 0.9556 (m-40) cc_final: 0.8793 (t0) REVERT: D 96 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8885 (mtm180) REVERT: D 103 LEU cc_start: 0.9523 (mt) cc_final: 0.9246 (mt) REVERT: E 39 HIS cc_start: 0.8386 (m90) cc_final: 0.7916 (m90) REVERT: E 41 TYR cc_start: 0.8518 (m-80) cc_final: 0.8215 (m-80) REVERT: E 74 ILE cc_start: 0.9693 (mt) cc_final: 0.9346 (tt) REVERT: E 93 GLN cc_start: 0.9416 (tt0) cc_final: 0.9137 (tt0) REVERT: E 99 TYR cc_start: 0.9451 (t80) cc_final: 0.9108 (t80) REVERT: E 117 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9272 (p) REVERT: F 35 ARG cc_start: 0.9746 (ttm170) cc_final: 0.9431 (ttm110) REVERT: F 49 LEU cc_start: 0.9766 (mm) cc_final: 0.9461 (tt) REVERT: F 53 GLU cc_start: 0.9140 (tp30) cc_final: 0.8529 (tp30) REVERT: F 54 THR cc_start: 0.9664 (m) cc_final: 0.9426 (p) REVERT: F 59 LYS cc_start: 0.9783 (tttm) cc_final: 0.9460 (tppp) REVERT: F 64 ASN cc_start: 0.9660 (m-40) cc_final: 0.9010 (t0) REVERT: F 84 MET cc_start: 0.9256 (mmm) cc_final: 0.8371 (mmm) REVERT: F 85 ASP cc_start: 0.9078 (m-30) cc_final: 0.8740 (t70) REVERT: G 25 PHE cc_start: 0.9254 (m-80) cc_final: 0.8606 (m-10) REVERT: G 27 VAL cc_start: 0.8578 (m) cc_final: 0.8258 (p) REVERT: G 39 TYR cc_start: 0.9000 (m-80) cc_final: 0.8666 (m-80) REVERT: G 84 GLN cc_start: 0.9400 (tp40) cc_final: 0.9180 (tp40) REVERT: G 89 ASN cc_start: 0.9649 (m-40) cc_final: 0.9425 (m110) REVERT: G 94 ASN cc_start: 0.9700 (t0) cc_final: 0.9321 (m110) REVERT: G 95 LYS cc_start: 0.9631 (mttt) cc_final: 0.9426 (mttt) REVERT: G 101 THR cc_start: 0.9688 (m) cc_final: 0.9360 (p) REVERT: G 102 ILE cc_start: 0.9641 (mt) cc_final: 0.9310 (mt) REVERT: G 107 VAL cc_start: 0.8488 (t) cc_final: 0.8168 (m) REVERT: H 34 TYR cc_start: 0.9633 (m-80) cc_final: 0.9218 (m-10) REVERT: H 59 MET cc_start: 0.9617 (mmm) cc_final: 0.9205 (mmm) REVERT: H 68 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9230 (tm-30) REVERT: H 73 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8920 (mm-30) REVERT: H 103 LEU cc_start: 0.9700 (mt) cc_final: 0.9469 (mt) REVERT: S 103 CYS cc_start: 0.5620 (t) cc_final: 0.5356 (t) REVERT: S 203 ASN cc_start: 0.9452 (t0) cc_final: 0.9093 (m-40) REVERT: S 276 LEU cc_start: 0.9569 (tp) cc_final: 0.9250 (pt) REVERT: S 278 MET cc_start: 0.6685 (mmm) cc_final: 0.6442 (mmm) outliers start: 4 outliers final: 0 residues processed: 385 average time/residue: 0.3467 time to fit residues: 178.5926 Evaluate side-chains 239 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C -32 GLN C 24 GLN D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 24 GLN G 38 ASN H 60 ASN S 171 ASN S 215 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15161 Z= 0.275 Angle : 0.638 12.559 21702 Z= 0.375 Chirality : 0.038 0.156 2447 Planarity : 0.005 0.055 1760 Dihedral : 30.101 173.004 4337 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.34 % Allowed : 4.18 % Favored : 95.48 % 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: 0.48 (0.26), residues: 1033 helix: 1.50 (0.21), residues: 571 sheet: -0.66 (0.61), residues: 66 loop : -1.28 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 135 HIS 0.011 0.002 HIS B 75 PHE 0.014 0.001 PHE H 67 TYR 0.022 0.002 TYR D 80 ARG 0.007 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 289 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8337 (mm) cc_final: 0.7486 (pp) REVERT: A 64 LYS cc_start: 0.9522 (mppt) cc_final: 0.9055 (mmtm) REVERT: A 68 GLN cc_start: 0.9784 (tt0) cc_final: 0.9343 (tm-30) REVERT: A 80 THR cc_start: 0.9490 (m) cc_final: 0.9262 (p) REVERT: A 81 ASP cc_start: 0.8912 (t0) cc_final: 0.8584 (t0) REVERT: A 90 MET cc_start: 0.9735 (tpt) cc_final: 0.9422 (tpt) REVERT: A 120 MET cc_start: 0.9437 (tpt) cc_final: 0.9206 (tpp) REVERT: B 44 LYS cc_start: 0.9496 (tttt) cc_final: 0.9276 (ttmt) REVERT: B 49 LEU cc_start: 0.9517 (mt) cc_final: 0.9290 (mm) REVERT: B 68 ASP cc_start: 0.9555 (m-30) cc_final: 0.9342 (m-30) REVERT: B 84 MET cc_start: 0.9326 (mmt) cc_final: 0.8162 (mmm) REVERT: B 85 ASP cc_start: 0.8995 (m-30) cc_final: 0.8587 (t70) REVERT: B 88 TYR cc_start: 0.9435 (m-10) cc_final: 0.8796 (m-80) REVERT: C 39 TYR cc_start: 0.9081 (m-80) cc_final: 0.8143 (m-80) REVERT: C 78 ILE cc_start: 0.9607 (mt) cc_final: 0.9337 (tp) REVERT: C 83 LEU cc_start: 0.9560 (mt) cc_final: 0.9319 (mt) REVERT: C 90 ASP cc_start: 0.8991 (t70) cc_final: 0.8674 (t0) REVERT: C 91 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8966 (mp0) REVERT: C 110 ASN cc_start: 0.9458 (t0) cc_final: 0.8951 (m110) REVERT: C 111 ILE cc_start: 0.9235 (mt) cc_final: 0.8927 (mm) REVERT: C 112 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8106 (tm-30) REVERT: D 34 TYR cc_start: 0.9199 (m-80) cc_final: 0.8979 (m-80) REVERT: D 54 LYS cc_start: 0.9590 (mppt) cc_final: 0.9316 (mppt) REVERT: D 59 MET cc_start: 0.9627 (mmp) cc_final: 0.9355 (mmm) REVERT: D 64 ASN cc_start: 0.9525 (m-40) cc_final: 0.9108 (t0) REVERT: D 68 GLU cc_start: 0.9343 (mp0) cc_final: 0.8721 (mm-30) REVERT: E 36 MET cc_start: 0.9277 (mtm) cc_final: 0.8787 (mtt) REVERT: E 39 HIS cc_start: 0.8500 (m90) cc_final: 0.8047 (m90) REVERT: E 56 LYS cc_start: 0.9373 (pttt) cc_final: 0.9027 (pptt) REVERT: E 73 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9195 (mm-30) REVERT: E 85 GLN cc_start: 0.9367 (mt0) cc_final: 0.9146 (mt0) REVERT: E 90 MET cc_start: 0.9225 (mmp) cc_final: 0.8904 (mmp) REVERT: E 120 MET cc_start: 0.9225 (mmp) cc_final: 0.8529 (mmm) REVERT: F 35 ARG cc_start: 0.9742 (ttm170) cc_final: 0.9436 (ttm110) REVERT: F 37 LEU cc_start: 0.9889 (mm) cc_final: 0.9661 (mm) REVERT: F 49 LEU cc_start: 0.9777 (mm) cc_final: 0.8809 (tp) REVERT: F 54 THR cc_start: 0.9713 (m) cc_final: 0.9432 (p) REVERT: F 59 LYS cc_start: 0.9804 (tttm) cc_final: 0.9601 (tppp) REVERT: F 64 ASN cc_start: 0.9653 (m-40) cc_final: 0.9254 (t0) REVERT: F 68 ASP cc_start: 0.9228 (m-30) cc_final: 0.8865 (m-30) REVERT: F 85 ASP cc_start: 0.9221 (m-30) cc_final: 0.8869 (m-30) REVERT: F 98 TYR cc_start: 0.8717 (m-80) cc_final: 0.8393 (m-10) REVERT: G 25 PHE cc_start: 0.9378 (m-80) cc_final: 0.8998 (m-10) REVERT: G 61 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9110 (mm-30) REVERT: G 78 ILE cc_start: 0.9781 (mm) cc_final: 0.9396 (tp) REVERT: G 92 GLU cc_start: 0.9070 (mp0) cc_final: 0.8649 (mt-10) REVERT: G 94 ASN cc_start: 0.9736 (t0) cc_final: 0.9302 (m110) REVERT: G 95 LYS cc_start: 0.9645 (mttt) cc_final: 0.9436 (mttt) REVERT: G 101 THR cc_start: 0.9601 (m) cc_final: 0.9327 (p) REVERT: G 104 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8609 (tp-100) REVERT: H 34 TYR cc_start: 0.9680 (m-80) cc_final: 0.9329 (m-10) REVERT: H 59 MET cc_start: 0.9553 (mmm) cc_final: 0.9109 (mmp) REVERT: H 68 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9144 (tm-30) REVERT: H 76 ARG cc_start: 0.8741 (ptp90) cc_final: 0.8457 (ptp90) REVERT: S 103 CYS cc_start: 0.6203 (t) cc_final: 0.5980 (t) REVERT: S 203 ASN cc_start: 0.9492 (t0) cc_final: 0.9195 (m-40) REVERT: S 223 MET cc_start: 0.8124 (tmm) cc_final: 0.7914 (tmm) REVERT: S 239 LEU cc_start: 0.8039 (tp) cc_final: 0.7816 (tp) outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 0.3347 time to fit residues: 133.7555 Evaluate side-chains 213 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 60 ASN S 164 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15161 Z= 0.278 Angle : 0.612 8.660 21702 Z= 0.362 Chirality : 0.037 0.155 2447 Planarity : 0.005 0.055 1760 Dihedral : 30.465 178.208 4337 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % 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: 0.57 (0.26), residues: 1033 helix: 1.43 (0.21), residues: 574 sheet: -0.65 (0.63), residues: 67 loop : -1.00 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 270 HIS 0.012 0.002 HIS B 75 PHE 0.011 0.001 PHE A 84 TYR 0.023 0.002 TYR F 88 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9302 (mm-30) REVERT: A 60 LEU cc_start: 0.8616 (mm) cc_final: 0.7944 (mm) REVERT: A 64 LYS cc_start: 0.9566 (mppt) cc_final: 0.9279 (mmtm) REVERT: A 65 LEU cc_start: 0.9709 (mm) cc_final: 0.9441 (mt) REVERT: A 68 GLN cc_start: 0.9783 (tt0) cc_final: 0.9284 (tm-30) REVERT: A 80 THR cc_start: 0.9492 (m) cc_final: 0.9266 (p) REVERT: A 81 ASP cc_start: 0.8979 (t0) cc_final: 0.8713 (t0) REVERT: A 90 MET cc_start: 0.9753 (tpt) cc_final: 0.9344 (tpt) REVERT: B 44 LYS cc_start: 0.9478 (tttt) cc_final: 0.9184 (ttmt) REVERT: B 59 LYS cc_start: 0.9645 (tptt) cc_final: 0.9388 (ttpp) REVERT: B 64 ASN cc_start: 0.9578 (m-40) cc_final: 0.9153 (t0) REVERT: B 68 ASP cc_start: 0.9549 (m-30) cc_final: 0.9312 (m-30) REVERT: B 70 VAL cc_start: 0.9637 (p) cc_final: 0.9029 (p) REVERT: B 84 MET cc_start: 0.9403 (mmt) cc_final: 0.8256 (mmm) REVERT: B 85 ASP cc_start: 0.9021 (m-30) cc_final: 0.8629 (t70) REVERT: B 88 TYR cc_start: 0.9543 (m-10) cc_final: 0.8962 (m-80) REVERT: C 24 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8528 (tp40) REVERT: C 39 TYR cc_start: 0.9169 (m-80) cc_final: 0.8571 (m-80) REVERT: C 56 GLU cc_start: 0.9256 (pp20) cc_final: 0.9028 (pp20) REVERT: C 62 ILE cc_start: 0.9752 (pt) cc_final: 0.9540 (pt) REVERT: C 78 ILE cc_start: 0.9701 (mt) cc_final: 0.9447 (tp) REVERT: C 83 LEU cc_start: 0.9571 (mt) cc_final: 0.9305 (mt) REVERT: C 90 ASP cc_start: 0.9045 (t70) cc_final: 0.8832 (t0) REVERT: C 91 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9022 (mp0) REVERT: C 96 LEU cc_start: 0.9192 (mt) cc_final: 0.8823 (mt) REVERT: C 101 THR cc_start: 0.9393 (m) cc_final: 0.9031 (t) REVERT: C 110 ASN cc_start: 0.9420 (t0) cc_final: 0.9000 (m110) REVERT: C 111 ILE cc_start: 0.9197 (mt) cc_final: 0.8979 (mm) REVERT: D 34 TYR cc_start: 0.9296 (m-80) cc_final: 0.9068 (m-80) REVERT: D 56 MET cc_start: 0.9622 (tpp) cc_final: 0.9390 (tpp) REVERT: D 59 MET cc_start: 0.9633 (mmp) cc_final: 0.9323 (mmm) REVERT: D 64 ASN cc_start: 0.9450 (m-40) cc_final: 0.9149 (t0) REVERT: D 68 GLU cc_start: 0.9356 (mp0) cc_final: 0.8800 (mm-30) REVERT: E 36 MET cc_start: 0.9267 (mtm) cc_final: 0.8852 (mtt) REVERT: E 39 HIS cc_start: 0.8586 (m90) cc_final: 0.8049 (m90) REVERT: E 79 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9255 (tmtt) REVERT: E 105 GLU cc_start: 0.9570 (tp30) cc_final: 0.9063 (tm-30) REVERT: E 120 MET cc_start: 0.9296 (mmp) cc_final: 0.8899 (mmm) REVERT: F 35 ARG cc_start: 0.9692 (ttm170) cc_final: 0.9370 (ttm110) REVERT: F 37 LEU cc_start: 0.9889 (mm) cc_final: 0.9680 (mm) REVERT: F 49 LEU cc_start: 0.9660 (mm) cc_final: 0.9308 (tp) REVERT: F 54 THR cc_start: 0.9692 (m) cc_final: 0.9462 (p) REVERT: F 63 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9321 (mt-10) REVERT: F 64 ASN cc_start: 0.9655 (m-40) cc_final: 0.9179 (t0) REVERT: F 68 ASP cc_start: 0.9198 (m-30) cc_final: 0.8745 (m-30) REVERT: F 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8885 (m-30) REVERT: F 96 THR cc_start: 0.9160 (p) cc_final: 0.8903 (p) REVERT: G 25 PHE cc_start: 0.9483 (m-80) cc_final: 0.9276 (m-10) REVERT: G 61 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9076 (mm-30) REVERT: G 78 ILE cc_start: 0.9835 (mm) cc_final: 0.9442 (tp) REVERT: G 92 GLU cc_start: 0.9080 (mp0) cc_final: 0.8568 (mt-10) REVERT: G 94 ASN cc_start: 0.9724 (t0) cc_final: 0.9373 (m-40) REVERT: G 101 THR cc_start: 0.9569 (m) cc_final: 0.9236 (p) REVERT: H 59 MET cc_start: 0.9647 (mmm) cc_final: 0.9125 (mmp) REVERT: H 103 LEU cc_start: 0.9616 (mt) cc_final: 0.9353 (mt) REVERT: S 113 LEU cc_start: 0.8950 (mp) cc_final: 0.8423 (mt) REVERT: S 203 ASN cc_start: 0.9624 (t0) cc_final: 0.9288 (m-40) REVERT: S 223 MET cc_start: 0.8273 (tmm) cc_final: 0.7995 (tmm) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.3082 time to fit residues: 114.0261 Evaluate side-chains 206 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN H 92 GLN S 175 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15161 Z= 0.180 Angle : 0.577 8.068 21702 Z= 0.342 Chirality : 0.036 0.146 2447 Planarity : 0.004 0.058 1760 Dihedral : 30.041 176.239 4337 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 0.62 (0.26), residues: 1033 helix: 1.47 (0.22), residues: 580 sheet: -0.42 (0.59), residues: 76 loop : -1.06 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 270 HIS 0.008 0.001 HIS B 75 PHE 0.010 0.001 PHE B 61 TYR 0.042 0.002 TYR F 88 ARG 0.006 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9277 (mm-30) REVERT: A 60 LEU cc_start: 0.8834 (mm) cc_final: 0.8437 (mm) REVERT: A 64 LYS cc_start: 0.9626 (mppt) cc_final: 0.9318 (mmtm) REVERT: A 65 LEU cc_start: 0.9672 (mm) cc_final: 0.8953 (tp) REVERT: A 68 GLN cc_start: 0.9751 (tt0) cc_final: 0.9550 (pp30) REVERT: A 80 THR cc_start: 0.9452 (m) cc_final: 0.9203 (p) REVERT: A 81 ASP cc_start: 0.8937 (t0) cc_final: 0.8672 (t0) REVERT: A 90 MET cc_start: 0.9767 (tpt) cc_final: 0.8752 (tpp) REVERT: A 94 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8869 (mm-30) REVERT: A 97 GLU cc_start: 0.9129 (pm20) cc_final: 0.8908 (pm20) REVERT: A 120 MET cc_start: 0.9573 (tpp) cc_final: 0.9295 (tpp) REVERT: B 44 LYS cc_start: 0.9454 (tttt) cc_final: 0.9221 (ttmm) REVERT: B 85 ASP cc_start: 0.9207 (m-30) cc_final: 0.8750 (t0) REVERT: C 39 TYR cc_start: 0.9092 (m-80) cc_final: 0.8621 (m-80) REVERT: C 56 GLU cc_start: 0.9271 (pp20) cc_final: 0.8985 (pp20) REVERT: C 78 ILE cc_start: 0.9651 (mt) cc_final: 0.9302 (tp) REVERT: C 83 LEU cc_start: 0.9578 (mt) cc_final: 0.9339 (mt) REVERT: C 90 ASP cc_start: 0.9220 (t70) cc_final: 0.8496 (t70) REVERT: C 96 LEU cc_start: 0.9035 (mt) cc_final: 0.8727 (mt) REVERT: C 110 ASN cc_start: 0.9250 (t0) cc_final: 0.8765 (m-40) REVERT: D 34 TYR cc_start: 0.9278 (m-80) cc_final: 0.9075 (m-80) REVERT: D 40 LYS cc_start: 0.9465 (mttt) cc_final: 0.9223 (ptpt) REVERT: D 56 MET cc_start: 0.9647 (tpp) cc_final: 0.9390 (tpp) REVERT: D 59 MET cc_start: 0.9668 (mmp) cc_final: 0.9237 (mmm) REVERT: D 64 ASN cc_start: 0.9370 (m-40) cc_final: 0.9109 (t0) REVERT: E 36 MET cc_start: 0.9311 (mtm) cc_final: 0.8838 (mtt) REVERT: E 39 HIS cc_start: 0.8491 (m90) cc_final: 0.7936 (m90) REVERT: E 56 LYS cc_start: 0.9324 (pptt) cc_final: 0.8977 (pptt) REVERT: E 62 ILE cc_start: 0.9183 (tp) cc_final: 0.8856 (pt) REVERT: E 74 ILE cc_start: 0.9823 (tp) cc_final: 0.9503 (tt) REVERT: E 79 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9297 (tmtt) REVERT: E 86 SER cc_start: 0.9533 (p) cc_final: 0.9259 (p) REVERT: E 97 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9292 (mm-30) REVERT: E 120 MET cc_start: 0.9417 (mmp) cc_final: 0.8919 (mmm) REVERT: F 31 LYS cc_start: 0.9744 (ttpt) cc_final: 0.9527 (mmtm) REVERT: F 35 ARG cc_start: 0.9693 (ttm170) cc_final: 0.9354 (mtm-85) REVERT: F 44 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8833 (mtmt) REVERT: F 49 LEU cc_start: 0.9613 (mm) cc_final: 0.9390 (tp) REVERT: F 54 THR cc_start: 0.9648 (m) cc_final: 0.9387 (p) REVERT: F 63 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9201 (mt-10) REVERT: F 64 ASN cc_start: 0.9672 (m-40) cc_final: 0.9189 (t0) REVERT: F 68 ASP cc_start: 0.9153 (m-30) cc_final: 0.8702 (m-30) REVERT: F 85 ASP cc_start: 0.9237 (m-30) cc_final: 0.8961 (m-30) REVERT: G 25 PHE cc_start: 0.9401 (m-80) cc_final: 0.9038 (m-10) REVERT: G 61 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9101 (mm-30) REVERT: G 92 GLU cc_start: 0.9048 (mp0) cc_final: 0.8747 (mt-10) REVERT: G 94 ASN cc_start: 0.9698 (t0) cc_final: 0.9355 (m-40) REVERT: G 95 LYS cc_start: 0.9377 (mtmm) cc_final: 0.9142 (mttp) REVERT: G 101 THR cc_start: 0.9588 (m) cc_final: 0.9328 (p) REVERT: G 102 ILE cc_start: 0.9530 (mt) cc_final: 0.9088 (tt) REVERT: G 104 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8651 (tp-100) REVERT: H 59 MET cc_start: 0.9582 (mmm) cc_final: 0.9172 (mmp) REVERT: H 73 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8878 (mm-30) REVERT: H 76 ARG cc_start: 0.8945 (ptp90) cc_final: 0.8539 (ptp90) REVERT: H 103 LEU cc_start: 0.9596 (mt) cc_final: 0.9357 (mt) REVERT: S 203 ASN cc_start: 0.9557 (t0) cc_final: 0.9018 (p0) REVERT: S 223 MET cc_start: 0.8325 (tmm) cc_final: 0.8058 (tmm) REVERT: S 278 MET cc_start: 0.7044 (ttt) cc_final: 0.6788 (ttt) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3036 time to fit residues: 109.5083 Evaluate side-chains 211 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15161 Z= 0.219 Angle : 0.574 5.974 21702 Z= 0.342 Chirality : 0.035 0.146 2447 Planarity : 0.004 0.058 1760 Dihedral : 30.225 177.837 4337 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 0.62 (0.26), residues: 1033 helix: 1.44 (0.22), residues: 574 sheet: -0.42 (0.59), residues: 76 loop : -0.96 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 270 HIS 0.008 0.001 HIS B 75 PHE 0.015 0.001 PHE D 62 TYR 0.042 0.002 TYR F 88 ARG 0.007 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9259 (mm-30) REVERT: A 60 LEU cc_start: 0.8849 (mm) cc_final: 0.8530 (mt) REVERT: A 64 LYS cc_start: 0.9655 (mppt) cc_final: 0.9351 (mmtm) REVERT: A 65 LEU cc_start: 0.9674 (mm) cc_final: 0.9471 (tp) REVERT: A 81 ASP cc_start: 0.8929 (t0) cc_final: 0.8674 (t0) REVERT: A 90 MET cc_start: 0.9756 (tpt) cc_final: 0.9344 (tpp) REVERT: A 108 ASN cc_start: 0.9709 (t0) cc_final: 0.9452 (m-40) REVERT: A 120 MET cc_start: 0.9529 (tpp) cc_final: 0.9156 (tpp) REVERT: A 122 LYS cc_start: 0.9750 (ptpp) cc_final: 0.9526 (ptpp) REVERT: B 43 VAL cc_start: 0.9533 (t) cc_final: 0.9116 (t) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9199 (ttmm) REVERT: B 59 LYS cc_start: 0.9673 (tppt) cc_final: 0.9406 (mmmt) REVERT: B 84 MET cc_start: 0.9323 (mmm) cc_final: 0.9086 (ppp) REVERT: B 85 ASP cc_start: 0.9208 (m-30) cc_final: 0.8899 (m-30) REVERT: C 39 TYR cc_start: 0.9170 (m-80) cc_final: 0.8584 (m-80) REVERT: C 56 GLU cc_start: 0.9259 (pp20) cc_final: 0.8978 (pp20) REVERT: C 62 ILE cc_start: 0.9684 (pt) cc_final: 0.9443 (pt) REVERT: C 78 ILE cc_start: 0.9682 (mt) cc_final: 0.9285 (tp) REVERT: C 83 LEU cc_start: 0.9603 (mt) cc_final: 0.9316 (mt) REVERT: C 110 ASN cc_start: 0.9242 (t0) cc_final: 0.8772 (m-40) REVERT: C 111 ILE cc_start: 0.9257 (mp) cc_final: 0.8746 (mm) REVERT: D 34 TYR cc_start: 0.9297 (m-80) cc_final: 0.9030 (m-80) REVERT: D 56 MET cc_start: 0.9638 (tpp) cc_final: 0.9387 (tpp) REVERT: D 59 MET cc_start: 0.9684 (mmp) cc_final: 0.9264 (mmm) REVERT: D 64 ASN cc_start: 0.9357 (m-40) cc_final: 0.8905 (t0) REVERT: D 67 PHE cc_start: 0.9433 (t80) cc_final: 0.9232 (t80) REVERT: D 68 GLU cc_start: 0.9298 (mp0) cc_final: 0.8618 (mm-30) REVERT: E 36 MET cc_start: 0.9233 (mtm) cc_final: 0.8759 (mtt) REVERT: E 39 HIS cc_start: 0.8602 (m90) cc_final: 0.8018 (m90) REVERT: E 50 GLU cc_start: 0.9685 (mp0) cc_final: 0.9408 (mp0) REVERT: E 56 LYS cc_start: 0.9387 (pptt) cc_final: 0.9062 (pptt) REVERT: E 62 ILE cc_start: 0.9336 (tp) cc_final: 0.8907 (pt) REVERT: E 79 LYS cc_start: 0.9602 (mmmm) cc_final: 0.9269 (tmtt) REVERT: E 86 SER cc_start: 0.9575 (p) cc_final: 0.9308 (p) REVERT: E 120 MET cc_start: 0.9383 (mmp) cc_final: 0.8878 (mmm) REVERT: F 31 LYS cc_start: 0.9736 (ttpt) cc_final: 0.9432 (tppt) REVERT: F 35 ARG cc_start: 0.9681 (ttm170) cc_final: 0.9363 (mtm-85) REVERT: F 44 LYS cc_start: 0.9296 (ttmt) cc_final: 0.8913 (mtmt) REVERT: F 49 LEU cc_start: 0.9584 (mm) cc_final: 0.9357 (tp) REVERT: F 63 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9205 (mt-10) REVERT: F 64 ASN cc_start: 0.9683 (m-40) cc_final: 0.9274 (t0) REVERT: F 68 ASP cc_start: 0.9133 (m-30) cc_final: 0.8673 (m-30) REVERT: F 74 GLU cc_start: 0.9084 (pp20) cc_final: 0.8865 (pp20) REVERT: F 84 MET cc_start: 0.9591 (mmm) cc_final: 0.9363 (mmm) REVERT: F 85 ASP cc_start: 0.9253 (m-30) cc_final: 0.8945 (m-30) REVERT: G 25 PHE cc_start: 0.9419 (m-80) cc_final: 0.9087 (m-10) REVERT: G 39 TYR cc_start: 0.8980 (m-10) cc_final: 0.8741 (m-10) REVERT: G 61 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9109 (mm-30) REVERT: G 94 ASN cc_start: 0.9700 (t0) cc_final: 0.9351 (m-40) REVERT: G 101 THR cc_start: 0.9595 (m) cc_final: 0.9367 (p) REVERT: H 40 LYS cc_start: 0.9666 (mttt) cc_final: 0.9422 (mtmm) REVERT: H 59 MET cc_start: 0.9670 (mmm) cc_final: 0.9185 (mmp) REVERT: S 203 ASN cc_start: 0.9579 (t0) cc_final: 0.9042 (p0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3115 time to fit residues: 106.6832 Evaluate side-chains 200 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15161 Z= 0.273 Angle : 0.599 6.966 21702 Z= 0.355 Chirality : 0.037 0.141 2447 Planarity : 0.005 0.058 1760 Dihedral : 30.613 179.427 4337 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 1.81 % Favored : 97.85 % 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: 0.47 (0.26), residues: 1033 helix: 1.31 (0.22), residues: 579 sheet: -0.69 (0.57), residues: 82 loop : -1.00 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 270 HIS 0.009 0.001 HIS B 75 PHE 0.015 0.001 PHE C 25 TYR 0.030 0.002 TYR B 88 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9284 (mm-30) REVERT: A 64 LYS cc_start: 0.9628 (mppt) cc_final: 0.9326 (mmtt) REVERT: A 65 LEU cc_start: 0.9682 (mm) cc_final: 0.9438 (tp) REVERT: A 68 GLN cc_start: 0.9774 (tt0) cc_final: 0.9259 (tm-30) REVERT: A 90 MET cc_start: 0.9751 (tpt) cc_final: 0.8770 (tpp) REVERT: A 94 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8924 (mm-30) REVERT: A 120 MET cc_start: 0.9600 (tpp) cc_final: 0.9399 (tpp) REVERT: B 44 LYS cc_start: 0.9449 (tttt) cc_final: 0.9147 (ttmt) REVERT: C 39 TYR cc_start: 0.9208 (m-80) cc_final: 0.8739 (m-80) REVERT: C 56 GLU cc_start: 0.9241 (pp20) cc_final: 0.8968 (pp20) REVERT: C 78 ILE cc_start: 0.9721 (mt) cc_final: 0.9439 (tp) REVERT: C 83 LEU cc_start: 0.9627 (mt) cc_final: 0.9374 (mt) REVERT: C 90 ASP cc_start: 0.9109 (t70) cc_final: 0.8095 (t70) REVERT: C 91 GLU cc_start: 0.9263 (mp0) cc_final: 0.9043 (mp0) REVERT: C 93 LEU cc_start: 0.9619 (mt) cc_final: 0.9337 (mt) REVERT: C 110 ASN cc_start: 0.9335 (t0) cc_final: 0.8818 (m110) REVERT: C 111 ILE cc_start: 0.9308 (mp) cc_final: 0.8806 (mm) REVERT: D 34 TYR cc_start: 0.9356 (m-80) cc_final: 0.9108 (m-80) REVERT: D 56 MET cc_start: 0.9649 (tpp) cc_final: 0.9411 (tpp) REVERT: D 58 ILE cc_start: 0.9859 (mm) cc_final: 0.9641 (mm) REVERT: D 59 MET cc_start: 0.9702 (mmp) cc_final: 0.9340 (mmm) REVERT: D 103 LEU cc_start: 0.9708 (mt) cc_final: 0.9478 (mt) REVERT: E 36 MET cc_start: 0.9220 (mtm) cc_final: 0.8722 (mtt) REVERT: E 39 HIS cc_start: 0.8667 (m90) cc_final: 0.8114 (m90) REVERT: E 50 GLU cc_start: 0.9654 (mp0) cc_final: 0.9434 (mp0) REVERT: E 56 LYS cc_start: 0.9427 (pptt) cc_final: 0.9133 (pptt) REVERT: E 62 ILE cc_start: 0.9285 (tp) cc_final: 0.8792 (pt) REVERT: E 79 LYS cc_start: 0.9622 (mmmm) cc_final: 0.9252 (tmtt) REVERT: E 86 SER cc_start: 0.9550 (p) cc_final: 0.9271 (p) REVERT: E 120 MET cc_start: 0.9298 (mmp) cc_final: 0.8728 (mmm) REVERT: F 35 ARG cc_start: 0.9679 (ttm170) cc_final: 0.9378 (ttm110) REVERT: F 44 LYS cc_start: 0.9316 (ttmt) cc_final: 0.8891 (mtmt) REVERT: F 49 LEU cc_start: 0.9567 (mm) cc_final: 0.9335 (tp) REVERT: F 63 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9209 (mt-10) REVERT: F 64 ASN cc_start: 0.9666 (m-40) cc_final: 0.9299 (t0) REVERT: F 68 ASP cc_start: 0.9219 (m-30) cc_final: 0.8770 (m-30) REVERT: F 74 GLU cc_start: 0.9163 (pp20) cc_final: 0.8953 (pp20) REVERT: F 85 ASP cc_start: 0.9166 (m-30) cc_final: 0.8718 (m-30) REVERT: F 88 TYR cc_start: 0.9308 (m-80) cc_final: 0.9090 (m-80) REVERT: G 25 PHE cc_start: 0.9453 (m-80) cc_final: 0.9123 (m-10) REVERT: G 39 TYR cc_start: 0.9025 (m-10) cc_final: 0.8799 (m-80) REVERT: G 61 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9089 (mm-30) REVERT: G 94 ASN cc_start: 0.9602 (t0) cc_final: 0.9190 (m-40) REVERT: G 101 THR cc_start: 0.9573 (m) cc_final: 0.9258 (p) REVERT: H 40 LYS cc_start: 0.9664 (mttt) cc_final: 0.9429 (mtmm) REVERT: H 59 MET cc_start: 0.9670 (mmm) cc_final: 0.9169 (mmp) REVERT: H 76 ARG cc_start: 0.9054 (ptp90) cc_final: 0.8750 (ptp90) REVERT: H 102 GLU cc_start: 0.9211 (tp30) cc_final: 0.8798 (tp30) REVERT: S 103 CYS cc_start: 0.5988 (t) cc_final: 0.5775 (t) REVERT: S 203 ASN cc_start: 0.9622 (t0) cc_final: 0.9096 (p0) REVERT: S 306 GLN cc_start: 0.5451 (OUTLIER) cc_final: 0.4868 (pp30) outliers start: 3 outliers final: 0 residues processed: 240 average time/residue: 0.3250 time to fit residues: 108.9163 Evaluate side-chains 198 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15161 Z= 0.249 Angle : 0.598 6.827 21702 Z= 0.354 Chirality : 0.037 0.165 2447 Planarity : 0.004 0.057 1760 Dihedral : 30.687 179.396 4337 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.46 (0.26), residues: 1033 helix: 1.27 (0.22), residues: 573 sheet: -0.59 (0.59), residues: 81 loop : -0.94 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 270 HIS 0.009 0.001 HIS B 75 PHE 0.011 0.001 PHE H 62 TYR 0.023 0.002 TYR B 88 ARG 0.011 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9280 (mm-30) REVERT: A 64 LYS cc_start: 0.9583 (mppt) cc_final: 0.9255 (mmtm) REVERT: A 65 LEU cc_start: 0.9668 (mm) cc_final: 0.9404 (tp) REVERT: A 68 GLN cc_start: 0.9760 (tt0) cc_final: 0.9239 (tm-30) REVERT: A 81 ASP cc_start: 0.8883 (t70) cc_final: 0.8629 (t0) REVERT: A 87 SER cc_start: 0.9688 (m) cc_final: 0.9346 (p) REVERT: A 90 MET cc_start: 0.9676 (tpt) cc_final: 0.9401 (tpp) REVERT: A 106 ASP cc_start: 0.8762 (m-30) cc_final: 0.8206 (m-30) REVERT: A 120 MET cc_start: 0.9528 (tpp) cc_final: 0.9213 (tpp) REVERT: B 44 LYS cc_start: 0.9446 (tttt) cc_final: 0.9200 (ttmm) REVERT: B 59 LYS cc_start: 0.9652 (tppt) cc_final: 0.9437 (mmmt) REVERT: B 85 ASP cc_start: 0.8657 (t0) cc_final: 0.8266 (t0) REVERT: B 88 TYR cc_start: 0.9463 (m-80) cc_final: 0.9057 (m-80) REVERT: C 39 TYR cc_start: 0.9224 (m-80) cc_final: 0.8673 (m-80) REVERT: C 56 GLU cc_start: 0.9233 (pp20) cc_final: 0.8977 (pp20) REVERT: C 78 ILE cc_start: 0.9697 (mt) cc_final: 0.9413 (tp) REVERT: C 83 LEU cc_start: 0.9633 (mt) cc_final: 0.9385 (mt) REVERT: C 90 ASP cc_start: 0.9157 (t70) cc_final: 0.8568 (t0) REVERT: D 34 TYR cc_start: 0.9325 (m-80) cc_final: 0.9102 (m-80) REVERT: D 56 MET cc_start: 0.9649 (tpp) cc_final: 0.9415 (tpp) REVERT: D 58 ILE cc_start: 0.9852 (mm) cc_final: 0.9619 (mm) REVERT: D 59 MET cc_start: 0.9689 (mmp) cc_final: 0.9353 (mmm) REVERT: D 103 LEU cc_start: 0.9710 (mt) cc_final: 0.9499 (mt) REVERT: E 36 MET cc_start: 0.9237 (mtm) cc_final: 0.8784 (mtt) REVERT: E 39 HIS cc_start: 0.8687 (m90) cc_final: 0.8127 (m90) REVERT: E 50 GLU cc_start: 0.9682 (mp0) cc_final: 0.9431 (mp0) REVERT: E 56 LYS cc_start: 0.9426 (pptt) cc_final: 0.9138 (pptt) REVERT: E 62 ILE cc_start: 0.9303 (tp) cc_final: 0.8816 (pt) REVERT: E 79 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9265 (tmtt) REVERT: E 86 SER cc_start: 0.9593 (p) cc_final: 0.9334 (p) REVERT: E 115 LYS cc_start: 0.9379 (mppt) cc_final: 0.9175 (mptt) REVERT: E 120 MET cc_start: 0.9296 (mmp) cc_final: 0.8746 (mmm) REVERT: F 35 ARG cc_start: 0.9671 (ttm170) cc_final: 0.9252 (ttm110) REVERT: F 44 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8898 (mtmt) REVERT: F 49 LEU cc_start: 0.9616 (mm) cc_final: 0.9380 (tp) REVERT: F 63 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9213 (mt-10) REVERT: F 64 ASN cc_start: 0.9675 (m-40) cc_final: 0.9196 (t0) REVERT: F 68 ASP cc_start: 0.9224 (m-30) cc_final: 0.8626 (m-30) REVERT: F 74 GLU cc_start: 0.9178 (pp20) cc_final: 0.8965 (pp20) REVERT: F 84 MET cc_start: 0.9648 (mmm) cc_final: 0.9331 (mmm) REVERT: F 88 TYR cc_start: 0.9444 (m-80) cc_final: 0.8153 (m-80) REVERT: G 25 PHE cc_start: 0.9440 (m-80) cc_final: 0.9103 (m-10) REVERT: G 39 TYR cc_start: 0.9026 (m-10) cc_final: 0.8691 (m-10) REVERT: G 61 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9070 (mm-30) REVERT: G 94 ASN cc_start: 0.9605 (t0) cc_final: 0.9249 (m-40) REVERT: H 40 LYS cc_start: 0.9636 (mttt) cc_final: 0.9410 (mtmm) REVERT: H 59 MET cc_start: 0.9665 (mmm) cc_final: 0.9158 (mmp) REVERT: H 76 ARG cc_start: 0.9059 (ptp90) cc_final: 0.8587 (ptp90) REVERT: S 103 CYS cc_start: 0.6121 (t) cc_final: 0.5905 (t) REVERT: S 203 ASN cc_start: 0.9636 (t0) cc_final: 0.9106 (p0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3113 time to fit residues: 102.2540 Evaluate side-chains 191 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 0.0050 overall best weight: 3.4002 ------------------------------------------------------------------------------- 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 38 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15161 Z= 0.237 Angle : 0.596 7.679 21702 Z= 0.351 Chirality : 0.037 0.167 2447 Planarity : 0.004 0.057 1760 Dihedral : 30.713 179.414 4337 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.11 % Allowed : 1.13 % Favored : 98.76 % 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: 0.33 (0.26), residues: 1033 helix: 1.15 (0.21), residues: 574 sheet: -0.56 (0.60), residues: 81 loop : -0.99 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 270 HIS 0.009 0.001 HIS B 75 PHE 0.010 0.001 PHE H 62 TYR 0.018 0.002 TYR F 88 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9545 (mppt) cc_final: 0.9230 (mmtm) REVERT: A 65 LEU cc_start: 0.9676 (mm) cc_final: 0.8997 (tp) REVERT: A 68 GLN cc_start: 0.9761 (tt0) cc_final: 0.9560 (pp30) REVERT: A 81 ASP cc_start: 0.8897 (t70) cc_final: 0.8637 (t0) REVERT: A 87 SER cc_start: 0.9685 (m) cc_final: 0.9313 (p) REVERT: A 90 MET cc_start: 0.9725 (tpt) cc_final: 0.9494 (tpp) REVERT: A 94 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8117 (tp30) REVERT: A 97 GLU cc_start: 0.9130 (pm20) cc_final: 0.8653 (pm20) REVERT: A 105 GLU cc_start: 0.8962 (pp20) cc_final: 0.8757 (pp20) REVERT: A 106 ASP cc_start: 0.8858 (m-30) cc_final: 0.8323 (m-30) REVERT: A 120 MET cc_start: 0.9582 (tpp) cc_final: 0.9332 (tpp) REVERT: B 44 LYS cc_start: 0.9423 (tttt) cc_final: 0.9186 (ttmm) REVERT: B 85 ASP cc_start: 0.8644 (t0) cc_final: 0.8428 (t0) REVERT: B 88 TYR cc_start: 0.9402 (m-80) cc_final: 0.9197 (m-80) REVERT: C 39 TYR cc_start: 0.9211 (m-80) cc_final: 0.8705 (m-80) REVERT: C 78 ILE cc_start: 0.9700 (mt) cc_final: 0.9393 (tp) REVERT: C 83 LEU cc_start: 0.9619 (mt) cc_final: 0.9393 (mt) REVERT: C 91 GLU cc_start: 0.9290 (mp0) cc_final: 0.8862 (pm20) REVERT: C 110 ASN cc_start: 0.9632 (t0) cc_final: 0.9314 (p0) REVERT: D 34 TYR cc_start: 0.9332 (m-80) cc_final: 0.9081 (m-80) REVERT: D 59 MET cc_start: 0.9679 (mmp) cc_final: 0.9397 (mmm) REVERT: D 65 ASP cc_start: 0.9252 (t70) cc_final: 0.8996 (t70) REVERT: D 68 GLU cc_start: 0.9071 (mp0) cc_final: 0.8723 (pm20) REVERT: D 91 ILE cc_start: 0.9669 (tp) cc_final: 0.9371 (pt) REVERT: D 96 ARG cc_start: 0.9296 (mtm-85) cc_final: 0.9001 (mtm-85) REVERT: D 103 LEU cc_start: 0.9717 (mt) cc_final: 0.9509 (mt) REVERT: E 36 MET cc_start: 0.9225 (mtm) cc_final: 0.8768 (mtt) REVERT: E 39 HIS cc_start: 0.8671 (m90) cc_final: 0.8142 (m90) REVERT: E 50 GLU cc_start: 0.9653 (mp0) cc_final: 0.9395 (mp0) REVERT: E 56 LYS cc_start: 0.9417 (pptt) cc_final: 0.9120 (pptt) REVERT: E 62 ILE cc_start: 0.9280 (tp) cc_final: 0.8792 (pt) REVERT: E 79 LYS cc_start: 0.9630 (mmmm) cc_final: 0.9288 (tmtt) REVERT: E 86 SER cc_start: 0.9653 (p) cc_final: 0.9435 (p) REVERT: E 115 LYS cc_start: 0.9393 (mppt) cc_final: 0.9174 (mptt) REVERT: E 120 MET cc_start: 0.9280 (mmp) cc_final: 0.8930 (mmm) REVERT: F 35 ARG cc_start: 0.9666 (ttm170) cc_final: 0.9257 (ttm110) REVERT: F 44 LYS cc_start: 0.9276 (ttmt) cc_final: 0.8830 (mtmt) REVERT: F 49 LEU cc_start: 0.9605 (mm) cc_final: 0.9359 (tp) REVERT: F 60 VAL cc_start: 0.9751 (t) cc_final: 0.9521 (p) REVERT: F 63 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9204 (mt-10) REVERT: F 64 ASN cc_start: 0.9671 (m-40) cc_final: 0.9320 (t0) REVERT: F 68 ASP cc_start: 0.9204 (m-30) cc_final: 0.8834 (m-30) REVERT: F 74 GLU cc_start: 0.9171 (pp20) cc_final: 0.8950 (pp20) REVERT: F 81 VAL cc_start: 0.9764 (t) cc_final: 0.9550 (t) REVERT: F 84 MET cc_start: 0.9452 (mmm) cc_final: 0.9052 (mmm) REVERT: F 88 TYR cc_start: 0.8957 (m-80) cc_final: 0.8651 (m-80) REVERT: G 25 PHE cc_start: 0.9486 (m-80) cc_final: 0.9080 (m-10) REVERT: G 39 TYR cc_start: 0.9040 (m-10) cc_final: 0.8639 (m-10) REVERT: G 61 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9071 (mm-30) REVERT: G 94 ASN cc_start: 0.9606 (t0) cc_final: 0.9238 (m-40) REVERT: H 59 MET cc_start: 0.9654 (mmm) cc_final: 0.9180 (mmp) REVERT: H 99 LEU cc_start: 0.9049 (mt) cc_final: 0.8829 (mt) REVERT: S 103 CYS cc_start: 0.6167 (t) cc_final: 0.5963 (t) REVERT: S 203 ASN cc_start: 0.9631 (t0) cc_final: 0.9112 (p0) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3136 time to fit residues: 103.4184 Evaluate side-chains 188 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 40.0000 chunk 115 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 44 GLN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15161 Z= 0.349 Angle : 0.660 7.529 21702 Z= 0.387 Chirality : 0.039 0.157 2447 Planarity : 0.005 0.054 1760 Dihedral : 31.214 178.932 4337 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.21 (0.26), residues: 1033 helix: 1.01 (0.21), residues: 573 sheet: -0.83 (0.65), residues: 72 loop : -0.91 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 270 HIS 0.011 0.002 HIS B 75 PHE 0.014 0.002 PHE E 84 TYR 0.036 0.002 TYR F 88 ARG 0.011 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8765 (mt) cc_final: 0.8496 (mt) REVERT: A 65 LEU cc_start: 0.9670 (mm) cc_final: 0.9367 (tp) REVERT: A 68 GLN cc_start: 0.9764 (tt0) cc_final: 0.9251 (tm-30) REVERT: A 81 ASP cc_start: 0.8992 (t70) cc_final: 0.8772 (t0) REVERT: A 87 SER cc_start: 0.9735 (m) cc_final: 0.9437 (p) REVERT: A 90 MET cc_start: 0.9638 (tpt) cc_final: 0.8912 (tpp) REVERT: A 94 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8803 (mm-30) REVERT: A 106 ASP cc_start: 0.8883 (m-30) cc_final: 0.8334 (m-30) REVERT: A 120 MET cc_start: 0.9599 (tpp) cc_final: 0.9306 (tpp) REVERT: B 44 LYS cc_start: 0.9427 (tttt) cc_final: 0.9169 (ttmm) REVERT: B 85 ASP cc_start: 0.8700 (t0) cc_final: 0.8480 (t0) REVERT: C 39 TYR cc_start: 0.9347 (m-80) cc_final: 0.8889 (m-80) REVERT: C 78 ILE cc_start: 0.9716 (mt) cc_final: 0.9423 (tp) REVERT: C 83 LEU cc_start: 0.9650 (mt) cc_final: 0.9417 (mt) REVERT: C 91 GLU cc_start: 0.9307 (mp0) cc_final: 0.8905 (pm20) REVERT: C 101 THR cc_start: 0.9278 (m) cc_final: 0.8360 (m) REVERT: C 110 ASN cc_start: 0.9645 (t0) cc_final: 0.9190 (m110) REVERT: D 34 TYR cc_start: 0.9380 (m-80) cc_final: 0.9172 (m-80) REVERT: D 40 LYS cc_start: 0.9397 (mttt) cc_final: 0.9144 (mtmm) REVERT: D 58 ILE cc_start: 0.9842 (mm) cc_final: 0.9609 (mm) REVERT: D 59 MET cc_start: 0.9716 (mmp) cc_final: 0.9436 (mmm) REVERT: D 65 ASP cc_start: 0.9255 (t70) cc_final: 0.8980 (t70) REVERT: D 68 GLU cc_start: 0.9069 (mp0) cc_final: 0.8749 (pm20) REVERT: D 103 LEU cc_start: 0.9736 (mt) cc_final: 0.9522 (mt) REVERT: E 36 MET cc_start: 0.9210 (mtm) cc_final: 0.8773 (mtt) REVERT: E 39 HIS cc_start: 0.8654 (m90) cc_final: 0.8124 (m90) REVERT: E 50 GLU cc_start: 0.9659 (mp0) cc_final: 0.9396 (mp0) REVERT: E 56 LYS cc_start: 0.9443 (pptt) cc_final: 0.9149 (pptt) REVERT: E 62 ILE cc_start: 0.9303 (tp) cc_final: 0.8791 (pt) REVERT: E 86 SER cc_start: 0.9700 (p) cc_final: 0.9427 (p) REVERT: E 94 GLU cc_start: 0.9076 (tp30) cc_final: 0.8540 (tm-30) REVERT: E 105 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8955 (pp20) REVERT: E 115 LYS cc_start: 0.9364 (mppt) cc_final: 0.9156 (mptt) REVERT: E 118 THR cc_start: 0.9080 (m) cc_final: 0.8562 (p) REVERT: E 120 MET cc_start: 0.9217 (mmp) cc_final: 0.8694 (mmm) REVERT: F 31 LYS cc_start: 0.9701 (ttpt) cc_final: 0.9491 (mmtm) REVERT: F 35 ARG cc_start: 0.9659 (ttm170) cc_final: 0.9390 (mtm-85) REVERT: F 44 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8810 (mtmt) REVERT: F 49 LEU cc_start: 0.9574 (mm) cc_final: 0.9324 (tp) REVERT: F 63 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9153 (mp0) REVERT: F 64 ASN cc_start: 0.9649 (m-40) cc_final: 0.9221 (t0) REVERT: F 68 ASP cc_start: 0.9290 (m-30) cc_final: 0.8718 (m-30) REVERT: F 84 MET cc_start: 0.9507 (mmm) cc_final: 0.9073 (mmm) REVERT: G 25 PHE cc_start: 0.9420 (m-80) cc_final: 0.9098 (m-10) REVERT: G 39 TYR cc_start: 0.9142 (m-10) cc_final: 0.8848 (m-80) REVERT: G 61 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9079 (mm-30) REVERT: G 94 ASN cc_start: 0.9600 (t0) cc_final: 0.9195 (m-40) REVERT: H 59 MET cc_start: 0.9678 (mmm) cc_final: 0.9185 (mmp) REVERT: H 99 LEU cc_start: 0.9053 (mt) cc_final: 0.8813 (mt) REVERT: S 203 ASN cc_start: 0.9642 (t0) cc_final: 0.9322 (m-40) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3034 time to fit residues: 95.7704 Evaluate side-chains 181 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS S 175 GLN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15161 Z= 0.245 Angle : 0.607 6.192 21702 Z= 0.357 Chirality : 0.037 0.148 2447 Planarity : 0.004 0.057 1760 Dihedral : 31.037 179.190 4337 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.35 (0.26), residues: 1033 helix: 1.21 (0.22), residues: 573 sheet: -0.60 (0.61), residues: 81 loop : -1.05 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 270 HIS 0.008 0.001 HIS B 75 PHE 0.014 0.001 PHE H 62 TYR 0.024 0.002 TYR B 88 ARG 0.004 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8718 (mt) cc_final: 0.8106 (mt) REVERT: A 65 LEU cc_start: 0.9669 (mm) cc_final: 0.9380 (tp) REVERT: A 68 GLN cc_start: 0.9760 (tt0) cc_final: 0.9256 (tm-30) REVERT: A 81 ASP cc_start: 0.8977 (t70) cc_final: 0.8757 (t0) REVERT: A 87 SER cc_start: 0.9723 (m) cc_final: 0.9403 (p) REVERT: A 90 MET cc_start: 0.9606 (tpt) cc_final: 0.8869 (tpp) REVERT: A 94 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8864 (mm-30) REVERT: A 97 GLU cc_start: 0.9162 (pp20) cc_final: 0.8931 (pp20) REVERT: A 106 ASP cc_start: 0.8877 (m-30) cc_final: 0.8284 (m-30) REVERT: A 120 MET cc_start: 0.9586 (tpp) cc_final: 0.9312 (tpp) REVERT: B 44 LYS cc_start: 0.9385 (tttt) cc_final: 0.9149 (ttmm) REVERT: B 59 LYS cc_start: 0.9491 (pptt) cc_final: 0.9139 (pptt) REVERT: B 85 ASP cc_start: 0.8719 (t0) cc_final: 0.8507 (t0) REVERT: C 39 TYR cc_start: 0.9337 (m-80) cc_final: 0.8627 (m-80) REVERT: C 78 ILE cc_start: 0.9697 (mt) cc_final: 0.9383 (tp) REVERT: C 83 LEU cc_start: 0.9618 (mt) cc_final: 0.9395 (mt) REVERT: C 101 THR cc_start: 0.9210 (m) cc_final: 0.8152 (m) REVERT: C 110 ASN cc_start: 0.9652 (t0) cc_final: 0.9276 (m110) REVERT: D 34 TYR cc_start: 0.9334 (m-80) cc_final: 0.9088 (m-80) REVERT: D 59 MET cc_start: 0.9664 (mmp) cc_final: 0.9394 (mmm) REVERT: D 65 ASP cc_start: 0.9219 (t70) cc_final: 0.8903 (t70) REVERT: D 68 GLU cc_start: 0.8999 (mp0) cc_final: 0.8709 (pm20) REVERT: D 91 ILE cc_start: 0.9722 (tp) cc_final: 0.9397 (pt) REVERT: D 96 ARG cc_start: 0.9286 (mtm-85) cc_final: 0.8975 (mtm-85) REVERT: D 103 LEU cc_start: 0.9716 (mt) cc_final: 0.9496 (mt) REVERT: E 36 MET cc_start: 0.9225 (mtm) cc_final: 0.8739 (mtt) REVERT: E 39 HIS cc_start: 0.8608 (m90) cc_final: 0.8049 (m90) REVERT: E 50 GLU cc_start: 0.9658 (mp0) cc_final: 0.9363 (mp0) REVERT: E 56 LYS cc_start: 0.9424 (pptt) cc_final: 0.9122 (pptt) REVERT: E 62 ILE cc_start: 0.9315 (tp) cc_final: 0.8837 (pt) REVERT: E 86 SER cc_start: 0.9707 (p) cc_final: 0.9429 (p) REVERT: E 94 GLU cc_start: 0.9079 (tp30) cc_final: 0.8537 (tm-30) REVERT: E 105 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8887 (pp20) REVERT: E 115 LYS cc_start: 0.9391 (mppt) cc_final: 0.9182 (mptt) REVERT: E 118 THR cc_start: 0.9166 (m) cc_final: 0.8908 (m) REVERT: E 120 MET cc_start: 0.9223 (mmp) cc_final: 0.8754 (mmm) REVERT: F 31 LYS cc_start: 0.9696 (ttpt) cc_final: 0.9475 (mptt) REVERT: F 35 ARG cc_start: 0.9658 (ttm170) cc_final: 0.9388 (mtm-85) REVERT: F 44 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8868 (mtmt) REVERT: F 49 LEU cc_start: 0.9581 (mm) cc_final: 0.9322 (tp) REVERT: F 60 VAL cc_start: 0.9742 (t) cc_final: 0.9517 (p) REVERT: F 63 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9197 (mt-10) REVERT: F 64 ASN cc_start: 0.9653 (m-40) cc_final: 0.9353 (t0) REVERT: F 68 ASP cc_start: 0.9261 (m-30) cc_final: 0.8988 (m-30) REVERT: F 84 MET cc_start: 0.9465 (mmm) cc_final: 0.9038 (mmm) REVERT: F 88 TYR cc_start: 0.8963 (m-80) cc_final: 0.8707 (m-80) REVERT: F 93 GLN cc_start: 0.8647 (mt0) cc_final: 0.8234 (mp10) REVERT: F 97 LEU cc_start: 0.9412 (tt) cc_final: 0.8883 (tp) REVERT: G 25 PHE cc_start: 0.9423 (m-80) cc_final: 0.9072 (m-10) REVERT: G 39 TYR cc_start: 0.9123 (m-10) cc_final: 0.8907 (m-80) REVERT: G 61 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9093 (mm-30) REVERT: G 94 ASN cc_start: 0.9592 (t0) cc_final: 0.9176 (m-40) REVERT: H 59 MET cc_start: 0.9682 (mmm) cc_final: 0.9175 (mmp) REVERT: H 99 LEU cc_start: 0.9013 (mt) cc_final: 0.8791 (mt) REVERT: S 203 ASN cc_start: 0.9636 (t0) cc_final: 0.9285 (m110) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3049 time to fit residues: 96.6897 Evaluate side-chains 182 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 106 HIS S 175 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.040680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027807 restraints weight = 135507.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.028712 restraints weight = 77661.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.029282 restraints weight = 56238.988| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15161 Z= 0.216 Angle : 0.596 7.378 21702 Z= 0.349 Chirality : 0.036 0.138 2447 Planarity : 0.005 0.058 1760 Dihedral : 30.894 177.764 4337 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 0.44 (0.26), residues: 1033 helix: 1.29 (0.22), residues: 573 sheet: -0.44 (0.63), residues: 76 loop : -1.04 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 270 HIS 0.007 0.001 HIS B 75 PHE 0.016 0.001 PHE H 62 TYR 0.014 0.002 TYR A 99 ARG 0.011 0.000 ARG H 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.34 seconds wall clock time: 54 minutes 25.95 seconds (3265.95 seconds total)