Starting phenix.real_space_refine on Thu Dec 14 20:09:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2023/6kiv_9999_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8596 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 61 5.16 5 C 12166 2.51 5 N 3759 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Residue "N ARG 76": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N ARG 228": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "T TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20719 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2881 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 14, 'TRANS': 351} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13389 SG CYS K3957 39.155 70.820 42.538 1.00167.86 S ATOM 13403 SG CYS K3959 42.422 71.072 44.036 1.00163.71 S Time building chain proxies: 11.09, per 1000 atoms: 0.54 Number of scatterers: 20719 At special positions: 0 Unit cell: (151.51, 141.7, 117.72, 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 1 29.99 S 61 16.00 P 290 15.00 O 4442 8.00 N 3759 7.00 C 12166 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 23 sheets defined 27.6% alpha, 10.1% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 9.69 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 87 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.858A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.917A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 54 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 removed outlier: 4.201A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 87 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.461A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.664A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 3816 through 3830 removed outlier: 5.517A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3877 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'O' and resid 23 through 33 Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 56 through 58 No H-bonds generated for 'chain 'O' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 4.089A pdb=" N GLY K3832 " --> pdb=" O PHE K3844 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id= C, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.951A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 80 through 83 removed outlier: 4.002A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 112 through 115 removed outlier: 4.168A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 156 through 159 Processing sheet with id= H, first strand: chain 'N' and resid 174 through 177 removed outlier: 3.940A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 243 through 245 removed outlier: 3.877A pdb=" N GLU N 205 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER N 203 " --> pdb=" O ASN N 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.977A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 2 through 6 Processing sheet with id= L, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.114A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 314 through 316 removed outlier: 3.545A pdb=" N VAL T 316 " --> pdb=" O ILE T 472 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 325 through 327 removed outlier: 3.647A pdb=" N GLY T 325 " --> pdb=" O LEU T 398 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU T 398 " --> pdb=" O GLY T 325 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP T 327 " --> pdb=" O ILE T 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE T 396 " --> pdb=" O TRP T 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'T' and resid 372 through 374 removed outlier: 3.581A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 68 through 72 removed outlier: 3.929A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 101 through 104 removed outlier: 3.577A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 177 through 179 removed outlier: 5.738A pdb=" N ASP R 199 " --> pdb=" O CYS R 205 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS R 205 " --> pdb=" O ASP R 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'R' and resid 219 through 222 removed outlier: 3.615A pdb=" N LYS R 239 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'R' and resid 264 through 266 Processing sheet with id= V, first strand: chain 'R' and resid 153 through 156 Processing sheet with id= W, first strand: chain 'R' and resid 304 through 309 removed outlier: 7.428A pdb=" N ALA R 319 " --> pdb=" O ILE R 305 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR R 307 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA R 317 " --> pdb=" O THR R 307 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 10.33 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: 4052 1.33 - 1.45: 6267 1.45 - 1.57: 10731 1.57 - 1.69: 578 1.69 - 1.81: 88 Bond restraints: 21716 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C6 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.338 1.386 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 89.61 - 98.52: 10 98.52 - 107.43: 2740 107.43 - 116.34: 13589 116.34 - 125.25: 13075 125.25 - 134.15: 1171 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.89 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N GLN N 323 " pdb=" CA GLN N 323 " pdb=" C GLN N 323 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 10875 35.82 - 71.65: 1373 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12278 sinusoidal: 6877 harmonic: 5401 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 133.83 46.17 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA ASN K3779 " pdb=" C ASN K3779 " pdb=" N PHE K3780 " pdb=" CA PHE K3780 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -143.60 -36.40 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2253 0.046 - 0.092: 872 0.092 - 0.138: 258 0.138 - 0.184: 49 0.184 - 0.230: 6 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3435 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 32 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K3779 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" CG ASN K3779 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN K3779 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN K3779 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K3768 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C VAL K3768 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL K3768 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS K3769 " -0.015 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4499 2.79 - 3.32: 17455 3.32 - 3.85: 37486 3.85 - 4.37: 41580 4.37 - 4.90: 64188 Nonbonded interactions: 165208 Sorted by model distance: nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.263 2.440 nonbonded pdb=" OG SER R 96 " pdb=" OD1 ASP R 98 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.265 2.440 nonbonded pdb=" OG SER R 49 " pdb=" O SER R 63 " model vdw 2.268 2.440 ... (remaining 165203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 5.370 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 64.890 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21716 Z= 0.424 Angle : 0.904 12.590 30585 Z= 0.511 Chirality : 0.053 0.230 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 1830 helix: -1.38 (0.17), residues: 568 sheet: -2.89 (0.26), residues: 312 loop : -3.18 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.003 PHE N 189 TYR 0.031 0.003 TYR B 51 ARG 0.009 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.4369 time to fit residues: 311.0362 Evaluate side-chains 278 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 0.0570 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 38 ASN C 84 GLN C 94 ASN D 79 HIS G 89 ASN G 110 ASN N 79 HIS N 273 GLN N 328 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 381 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21716 Z= 0.271 Angle : 0.674 9.660 30585 Z= 0.379 Chirality : 0.042 0.196 3438 Planarity : 0.005 0.089 2870 Dihedral : 27.615 178.092 5203 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.33 % Allowed : 11.91 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.18), residues: 1830 helix: 0.43 (0.21), residues: 560 sheet: -2.72 (0.26), residues: 302 loop : -2.99 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 198 HIS 0.011 0.001 HIS R 44 PHE 0.018 0.002 PHE N 189 TYR 0.039 0.002 TYR B 51 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 312 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 45 residues processed: 355 average time/residue: 0.3433 time to fit residues: 184.1093 Evaluate side-chains 292 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1874 time to fit residues: 18.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 64 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 94 ASN E 55 GLN N 250 ASN N 273 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21716 Z= 0.220 Angle : 0.617 9.737 30585 Z= 0.349 Chirality : 0.041 0.172 3438 Planarity : 0.004 0.084 2870 Dihedral : 27.444 177.440 5203 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.94 % Allowed : 14.36 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1830 helix: 1.18 (0.22), residues: 558 sheet: -2.63 (0.26), residues: 301 loop : -2.79 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 59 HIS 0.008 0.001 HIS R 44 PHE 0.022 0.001 PHE N 189 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 304 average time/residue: 0.3445 time to fit residues: 158.1955 Evaluate side-chains 264 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 247 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2490 time to fit residues: 10.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.0670 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 54 optimal weight: 0.5980 overall best weight: 4.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 106 HIS K3839 HIS N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21716 Z= 0.337 Angle : 0.680 8.195 30585 Z= 0.380 Chirality : 0.043 0.205 3438 Planarity : 0.005 0.085 2870 Dihedral : 27.583 177.417 5203 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.26 % Allowed : 15.36 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 1830 helix: 0.92 (0.21), residues: 551 sheet: -2.47 (0.27), residues: 299 loop : -2.78 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 156 HIS 0.008 0.002 HIS F 75 PHE 0.021 0.002 PHE K3885 TYR 0.030 0.002 TYR F 88 ARG 0.004 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 250 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 35 residues processed: 282 average time/residue: 0.3464 time to fit residues: 147.8998 Evaluate side-chains 270 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1902 time to fit residues: 15.0986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 7.9990 chunk 114 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 171 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 overall best weight: 2.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** T 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21716 Z= 0.241 Angle : 0.618 7.343 30585 Z= 0.350 Chirality : 0.041 0.164 3438 Planarity : 0.004 0.091 2870 Dihedral : 27.458 175.977 5203 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.26 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 1830 helix: 1.18 (0.22), residues: 551 sheet: -2.44 (0.28), residues: 277 loop : -2.64 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 59 HIS 0.007 0.001 HIS R 44 PHE 0.017 0.001 PHE N 189 TYR 0.044 0.002 TYR F 88 ARG 0.009 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 279 average time/residue: 0.3639 time to fit residues: 155.0242 Evaluate side-chains 265 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2252 time to fit residues: 10.5509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 167 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 75 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21716 Z= 0.176 Angle : 0.581 11.165 30585 Z= 0.331 Chirality : 0.040 0.212 3438 Planarity : 0.004 0.085 2870 Dihedral : 27.273 175.660 5203 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.38 % Allowed : 18.75 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1830 helix: 1.54 (0.22), residues: 548 sheet: -2.36 (0.27), residues: 307 loop : -2.55 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 59 HIS 0.005 0.001 HIS R 44 PHE 0.017 0.001 PHE N 189 TYR 0.038 0.002 TYR H 80 ARG 0.009 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 290 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 299 average time/residue: 0.3323 time to fit residues: 150.0365 Evaluate side-chains 276 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2171 time to fit residues: 8.0062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 40.0000 chunk 112 optimal weight: 0.7980 chunk 200 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21716 Z= 0.287 Angle : 0.654 12.550 30585 Z= 0.364 Chirality : 0.042 0.212 3438 Planarity : 0.004 0.087 2870 Dihedral : 27.418 176.651 5203 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.69 % Allowed : 19.81 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1830 helix: 1.21 (0.22), residues: 547 sheet: -2.30 (0.27), residues: 307 loop : -2.56 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 156 HIS 0.006 0.001 HIS K3822 PHE 0.015 0.002 PHE N 206 TYR 0.057 0.002 TYR H 80 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 269 average time/residue: 0.3498 time to fit residues: 141.6758 Evaluate side-chains 250 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1812 time to fit residues: 7.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 0.0570 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3907 HIS ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21716 Z= 0.164 Angle : 0.600 11.996 30585 Z= 0.336 Chirality : 0.040 0.208 3438 Planarity : 0.004 0.083 2870 Dihedral : 27.130 175.145 5203 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.88 % Allowed : 20.63 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1830 helix: 1.65 (0.22), residues: 549 sheet: -2.11 (0.28), residues: 312 loop : -2.47 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 156 HIS 0.004 0.001 HIS R 44 PHE 0.014 0.001 PHE N 189 TYR 0.061 0.002 TYR H 80 ARG 0.004 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 287 average time/residue: 0.3275 time to fit residues: 145.6375 Evaluate side-chains 258 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1966 time to fit residues: 5.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.0470 chunk 192 optimal weight: 20.0000 chunk 175 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21716 Z= 0.317 Angle : 0.683 12.664 30585 Z= 0.378 Chirality : 0.042 0.215 3438 Planarity : 0.004 0.086 2870 Dihedral : 27.407 176.793 5203 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.13 % Allowed : 21.44 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.19), residues: 1830 helix: 1.05 (0.21), residues: 556 sheet: -2.18 (0.28), residues: 292 loop : -2.59 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP R 156 HIS 0.007 0.001 HIS K3822 PHE 0.012 0.002 PHE F 61 TYR 0.090 0.002 TYR H 80 ARG 0.005 0.001 ARG R 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 251 average time/residue: 0.3198 time to fit residues: 122.4852 Evaluate side-chains 245 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1731 time to fit residues: 5.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 165 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21716 Z= 0.341 Angle : 0.707 13.552 30585 Z= 0.390 Chirality : 0.043 0.210 3438 Planarity : 0.005 0.083 2870 Dihedral : 27.480 175.307 5203 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.82 % Allowed : 21.63 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1830 helix: 0.81 (0.22), residues: 545 sheet: -2.24 (0.28), residues: 305 loop : -2.62 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 156 HIS 0.007 0.001 HIS K3822 PHE 0.013 0.002 PHE N 259 TYR 0.110 0.003 TYR H 80 ARG 0.009 0.001 ARG H 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 242 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 250 average time/residue: 0.3497 time to fit residues: 133.7054 Evaluate side-chains 241 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1903 time to fit residues: 5.9166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 69 optimal weight: 0.0060 chunk 169 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.142196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107977 restraints weight = 53910.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108454 restraints weight = 33602.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109022 restraints weight = 25103.508| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21716 Z= 0.176 Angle : 0.635 11.154 30585 Z= 0.351 Chirality : 0.040 0.198 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.091 173.768 5203 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.38 % Allowed : 22.26 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1830 helix: 1.39 (0.22), residues: 555 sheet: -2.08 (0.28), residues: 311 loop : -2.46 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 156 HIS 0.008 0.001 HIS H 79 PHE 0.015 0.001 PHE N 189 TYR 0.087 0.002 TYR F 88 ARG 0.004 0.000 ARG R 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.71 seconds wall clock time: 72 minutes 32.04 seconds (4352.04 seconds total)