Starting phenix.real_space_refine (version: dev) on Fri Dec 16 06:22:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2022/6kiv_9999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2022/6kiv_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_2022/6kiv_9999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2022/6kiv_9999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2022/6kiv_9999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/12_2022/6kiv_9999_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4807/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: 11.73, per 1000 atoms: 0.57 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: 10.75 Conformation dependent library (CDL) restraints added in 2.2 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: 7.80 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: 9.71 Time building geometry restraints manager: 11.21 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: 10665 35.82 - 71.65: 1331 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12026 sinusoidal: 6625 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 12023 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 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. 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 6.090 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 67.130 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 22.522 179.114 8542 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.980 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: 0.4105 time to fit residues: 296.2779 Evaluate side-chains 278 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5607 ------------------------------------------------------------------------------- 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: 6.9990 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: 0.7557 moved from start: 0.2656 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= 0.275 Angle : 0.680 9.963 30585 Z= 0.382 Chirality : 0.042 0.159 3438 Planarity : 0.005 0.094 2870 Dihedral : 27.841 178.340 4951 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer Outliers : 4.01 % 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: -2.75 (0.18), residues: 1830 helix: 0.36 (0.21), residues: 564 sheet: -2.72 (0.26), residues: 302 loop : -3.00 (0.17), residues: 964 *********************** 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 375 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 311 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 44 residues processed: 350 average time/residue: 0.3224 time to fit residues: 171.0782 Evaluate side-chains 300 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 256 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1777 time to fit residues: 17.2418 ------------------------------------------------------------------------------- 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: 2.9990 chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 151 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3205 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= 0.247 Angle : 0.635 9.649 30585 Z= 0.358 Chirality : 0.041 0.192 3438 Planarity : 0.004 0.089 2870 Dihedral : 27.727 178.166 4951 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 2.13 % 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: 1.12 (0.22), residues: 555 sheet: -2.72 (0.26), residues: 306 loop : -2.83 (0.18), residues: 969 *********************** 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 326 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 292 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 312 average time/residue: 0.3334 time to fit residues: 158.3005 Evaluate side-chains 270 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2250 time to fit residues: 12.3510 ------------------------------------------------------------------------------- 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: 20.0000 chunk 142 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN D 106 HIS F 64 ASN F 75 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 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.077 21716 Z= 0.547 Angle : 0.854 10.694 30585 Z= 0.468 Chirality : 0.050 0.328 3438 Planarity : 0.006 0.087 2870 Dihedral : 28.277 178.357 4951 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.80 % Favored : 88.14 % Rotamer Outliers : 4.33 % 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: -2.96 (0.18), residues: 1830 helix: 0.05 (0.20), residues: 548 sheet: -2.65 (0.27), residues: 271 loop : -3.07 (0.17), residues: 1011 *********************** 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 314 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 245 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 37 residues processed: 290 average time/residue: 0.3281 time to fit residues: 145.8163 Evaluate side-chains 266 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1907 time to fit residues: 15.5516 ------------------------------------------------------------------------------- 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: 20.0000 chunk 114 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS R 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 21716 Z= 0.184 Angle : 0.611 9.783 30585 Z= 0.346 Chirality : 0.041 0.153 3438 Planarity : 0.004 0.080 2870 Dihedral : 27.752 174.243 4951 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 1.38 % 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: -2.08 (0.19), residues: 1830 helix: 1.23 (0.22), residues: 549 sheet: -2.64 (0.27), residues: 279 loop : -2.65 (0.18), residues: 1002 *********************** 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 304 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 296 average time/residue: 0.3060 time to fit residues: 139.7764 Evaluate side-chains 260 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 250 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1847 time to fit residues: 6.0053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 167 optimal weight: 50.0000 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4350 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= 0.270 Angle : 0.640 11.418 30585 Z= 0.360 Chirality : 0.042 0.316 3438 Planarity : 0.004 0.083 2870 Dihedral : 27.759 176.397 4951 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 2.76 % 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: -2.14 (0.19), residues: 1830 helix: 1.14 (0.22), residues: 548 sheet: -2.51 (0.27), residues: 291 loop : -2.70 (0.18), residues: 991 *********************** 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 297 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 253 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 274 average time/residue: 0.3129 time to fit residues: 132.0808 Evaluate side-chains 273 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2125 time to fit residues: 14.0821 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4506 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= 0.283 Angle : 0.660 10.186 30585 Z= 0.369 Chirality : 0.042 0.188 3438 Planarity : 0.004 0.083 2870 Dihedral : 27.752 176.319 4951 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 1.32 % 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: -2.14 (0.19), residues: 1830 helix: 1.00 (0.22), residues: 548 sheet: -2.30 (0.28), residues: 276 loop : -2.69 (0.18), residues: 1006 *********************** 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 281 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 268 average time/residue: 0.3055 time to fit residues: 126.3250 Evaluate side-chains 252 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1853 time to fit residues: 5.8671 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 0.0470 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 157 optimal weight: 0.0060 overall best weight: 0.4294 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 255 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4819 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= 0.160 Angle : 0.596 10.049 30585 Z= 0.335 Chirality : 0.040 0.157 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.441 175.261 4951 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.00 % 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 (0.19), residues: 1830 helix: 1.52 (0.22), residues: 550 sheet: -2.15 (0.28), residues: 303 loop : -2.51 (0.18), residues: 977 *********************** 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 311 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 295 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 302 average time/residue: 0.3324 time to fit residues: 155.2691 Evaluate side-chains 262 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 255 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1775 time to fit residues: 4.9433 ------------------------------------------------------------------------------- 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: 0.0270 chunk 192 optimal weight: 20.0000 chunk 175 optimal weight: 0.0670 chunk 186 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 overall best weight: 2.6182 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** 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 456 GLN ** R 170 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: 0.7574 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 21716 Z= 0.250 Angle : 0.647 11.417 30585 Z= 0.358 Chirality : 0.041 0.190 3438 Planarity : 0.004 0.085 2870 Dihedral : 27.591 177.127 4951 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 1.00 % 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: -1.84 (0.19), residues: 1830 helix: 1.20 (0.22), residues: 559 sheet: -1.99 (0.29), residues: 298 loop : -2.56 (0.18), residues: 973 *********************** 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 270 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 266 average time/residue: 0.3191 time to fit residues: 131.3021 Evaluate side-chains 245 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1893 time to fit residues: 4.2874 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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** ** R 170 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4991 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= 0.432 Angle : 0.767 14.913 30585 Z= 0.421 Chirality : 0.046 0.294 3438 Planarity : 0.005 0.086 2870 Dihedral : 27.941 177.122 4951 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.11 % Favored : 89.84 % Rotamer Outliers : 1.07 % 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: 0.56 (0.21), residues: 541 sheet: -2.12 (0.29), residues: 281 loop : -2.64 (0.18), residues: 1008 ********************** 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 253 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 246 average time/residue: 0.3299 time to fit residues: 125.2335 Evaluate side-chains 240 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1893 time to fit residues: 6.5182 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 0.3980 chunk 152 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 169 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.0060 chunk 145 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103973 restraints weight = 53547.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104441 restraints weight = 33109.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105325 restraints weight = 21944.264| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21716 Z= 0.185 Angle : 0.641 10.664 30585 Z= 0.354 Chirality : 0.041 0.174 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.552 174.440 4951 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.25 % 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: -1.78 (0.19), residues: 1830 helix: 1.31 (0.22), residues: 546 sheet: -2.07 (0.29), residues: 291 loop : -2.46 (0.18), residues: 993 =============================================================================== Job complete usr+sys time: 3640.16 seconds wall clock time: 67 minutes 22.80 seconds (4042.80 seconds total)