Starting phenix.real_space_refine on Thu Feb 15 08:20:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xke_33249/02_2024/7xke_33249_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3759 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5067 2.51 5 N 1365 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 392": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7922 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1905 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2034 Unusual residues: {'AND': 1} Classifications: {'peptide': 253, 'undetermined': 1, 'water': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 247, None: 2} Not linked: pdbres="ARG R 883 " pdbres="AND R1001 " Not linked: pdbres="AND R1001 " pdbres="HOH R1101 " Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 4.84, per 1000 atoms: 0.61 Number of scatterers: 7922 At special positions: 0 Unit cell: (93.628, 122.032, 93.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1440 8.00 N 1365 7.00 C 5067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 36.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 24 through 49 removed outlier: 3.954A pdb=" N GLN A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.854A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 619 through 644 Processing helix chain 'R' and resid 646 through 648 No H-bonds generated for 'chain 'R' and resid 646 through 648' Processing helix chain 'R' and resid 652 through 676 removed outlier: 3.811A pdb=" N GLN R 659 " --> pdb=" O LYS R 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 684 through 715 Processing helix chain 'R' and resid 726 through 734 removed outlier: 3.600A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 737 through 748 Processing helix chain 'R' and resid 750 through 753 removed outlier: 4.034A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 777 through 781 Processing helix chain 'R' and resid 783 through 809 Processing helix chain 'R' and resid 822 through 833 Processing helix chain 'R' and resid 836 through 845 Processing helix chain 'R' and resid 850 through 871 removed outlier: 3.801A pdb=" N THR R 861 " --> pdb=" O ALA R 857 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY R 864 " --> pdb=" O ASN R 860 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE R 865 " --> pdb=" O THR R 861 " (cutoff:3.500A) Processing helix chain 'R' and resid 876 through 882 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.908A pdb=" N ALA A 253 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 257 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 234 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY A 57 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 88 through 90 Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.816A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 5.953A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.774A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.592A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.742A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1267 1.31 - 1.44: 2275 1.44 - 1.56: 4470 1.56 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 8089 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.684 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.741 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.683 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.661 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.642 -0.111 2.00e-02 2.50e+03 3.07e+01 ... (remaining 8084 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.46: 156 106.46 - 113.35: 4410 113.35 - 120.24: 2821 120.24 - 127.14: 3504 127.14 - 134.03: 79 Bond angle restraints: 10970 Sorted by residual: angle pdb=" N TRP R 676 " pdb=" CA TRP R 676 " pdb=" C TRP R 676 " ideal model delta sigma weight residual 111.36 115.96 -4.60 1.09e+00 8.42e-01 1.78e+01 angle pdb=" N HIS R 710 " pdb=" CA HIS R 710 " pdb=" C HIS R 710 " ideal model delta sigma weight residual 111.07 107.12 3.95 1.07e+00 8.73e-01 1.36e+01 angle pdb=" N MET A 35 " pdb=" CA MET A 35 " pdb=" C MET A 35 " ideal model delta sigma weight residual 113.18 108.76 4.42 1.21e+00 6.83e-01 1.33e+01 angle pdb=" N LYS A 42 " pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 111.69 108.06 3.63 1.23e+00 6.61e-01 8.73e+00 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.16 114.42 -4.26 1.48e+00 4.57e-01 8.30e+00 ... (remaining 10965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4411 17.63 - 35.27: 328 35.27 - 52.90: 57 52.90 - 70.53: 8 70.53 - 88.16: 6 Dihedral angle restraints: 4810 sinusoidal: 1882 harmonic: 2928 Sorted by residual: dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -127.60 41.60 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG B 219 " pdb=" C ARG B 219 " pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta harmonic sigma weight residual 180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1142 0.073 - 0.146: 103 0.146 - 0.219: 2 0.219 - 0.292: 0 0.292 - 0.365: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.35 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.77 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C14 AND R1001 " pdb=" C13 AND R1001 " pdb=" C15 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.32 -2.49 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1246 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 34 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C LYS A 34 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 34 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 35 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO B 236 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 262 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ASP A 262 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP A 262 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 263 " -0.009 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 980 2.75 - 3.29: 7976 3.29 - 3.83: 13656 3.83 - 4.36: 15857 4.36 - 4.90: 27789 Nonbonded interactions: 66258 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.213 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.230 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.246 2.520 nonbonded pdb=" OG SER B 108 " pdb=" OD2 ASP B 154 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.262 2.440 ... (remaining 66253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.006 0.352 8089 Z= 0.395 Angle : 0.565 8.499 10970 Z= 0.312 Chirality : 0.044 0.365 1249 Planarity : 0.003 0.045 1383 Dihedral : 12.845 88.163 2909 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.24 % Allowed : 0.71 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 991 helix: 1.43 (0.28), residues: 376 sheet: -0.30 (0.35), residues: 226 loop : -0.88 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.001 PHE B 234 TYR 0.016 0.001 TYR A 358 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 0.977 Fit side-chains REVERT: A 45 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 278 ASN cc_start: 0.8593 (m-40) cc_final: 0.8274 (m110) REVERT: B 20 ASP cc_start: 0.8456 (m-30) cc_final: 0.8175 (m-30) REVERT: G 32 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7926 (tmtt) REVERT: G 36 ASP cc_start: 0.7910 (m-30) cc_final: 0.7478 (m-30) REVERT: G 42 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7443 (tm-30) REVERT: R 822 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7021 (tm-30) outliers start: 2 outliers final: 2 residues processed: 161 average time/residue: 1.5475 time to fit residues: 260.6873 Evaluate side-chains 122 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.167 Angle : 0.505 7.269 10970 Z= 0.267 Chirality : 0.040 0.138 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.281 46.351 1155 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.79 % Allowed : 12.38 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 991 helix: 1.77 (0.28), residues: 372 sheet: -0.26 (0.35), residues: 226 loop : -0.91 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.001 PHE R 856 TYR 0.014 0.001 TYR A 358 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.936 Fit side-chains REVERT: A 43 ASP cc_start: 0.7781 (m-30) cc_final: 0.7572 (m-30) REVERT: A 45 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 20 ASP cc_start: 0.8450 (m-30) cc_final: 0.8165 (m-30) REVERT: G 42 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7419 (tm-30) REVERT: N 31 ASN cc_start: 0.8904 (m110) cc_final: 0.8662 (m-40) REVERT: R 650 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7741 (mmp80) REVERT: R 659 GLN cc_start: 0.8406 (mp10) cc_final: 0.8101 (mm-40) REVERT: R 676 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.7384 (t-100) REVERT: R 809 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8335 (mttt) REVERT: R 822 GLN cc_start: 0.7469 (tm-30) cc_final: 0.6967 (tm-30) REVERT: R 853 MET cc_start: 0.7752 (tmm) cc_final: 0.7521 (tmm) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 1.4528 time to fit residues: 215.3292 Evaluate side-chains 133 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 628 CYS Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 651 ASP Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.163 Angle : 0.493 6.807 10970 Z= 0.259 Chirality : 0.039 0.146 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.137 44.272 1155 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.38 % Allowed : 15.00 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 991 helix: 1.79 (0.28), residues: 374 sheet: -0.27 (0.34), residues: 226 loop : -0.95 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE R 856 TYR 0.016 0.001 TYR A 358 ARG 0.007 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.911 Fit side-chains REVERT: A 43 ASP cc_start: 0.7687 (m-30) cc_final: 0.7460 (m-30) REVERT: A 45 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8160 (tm-30) REVERT: B 20 ASP cc_start: 0.8442 (m-30) cc_final: 0.8169 (m-30) REVERT: B 43 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 340 ASN cc_start: 0.7921 (t0) cc_final: 0.7509 (m-40) REVERT: G 42 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7482 (tm-30) REVERT: R 650 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7717 (mmp80) REVERT: R 659 GLN cc_start: 0.8402 (mp10) cc_final: 0.8114 (mm-40) REVERT: R 676 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.7399 (t-100) REVERT: R 809 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8272 (mttt) REVERT: R 822 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6878 (tm-30) outliers start: 20 outliers final: 8 residues processed: 143 average time/residue: 1.4552 time to fit residues: 218.9001 Evaluate side-chains 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 628 CYS Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8089 Z= 0.183 Angle : 0.500 7.161 10970 Z= 0.263 Chirality : 0.040 0.150 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.175 42.246 1155 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.62 % Allowed : 16.07 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 991 helix: 1.80 (0.28), residues: 375 sheet: -0.25 (0.34), residues: 221 loop : -0.95 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 832 TYR 0.014 0.001 TYR A 358 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7726 (m-30) cc_final: 0.7478 (m-30) REVERT: A 45 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 20 ASP cc_start: 0.8444 (m-30) cc_final: 0.8172 (m-30) REVERT: B 43 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 340 ASN cc_start: 0.7741 (t0) cc_final: 0.7422 (t0) REVERT: G 42 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7463 (tm-30) REVERT: R 650 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7652 (mmp80) REVERT: R 651 ASP cc_start: 0.8625 (p0) cc_final: 0.8237 (p0) REVERT: R 659 GLN cc_start: 0.8402 (mp10) cc_final: 0.8113 (mm-40) REVERT: R 676 TRP cc_start: 0.7568 (OUTLIER) cc_final: 0.7329 (t-100) REVERT: R 726 TYR cc_start: 0.8097 (t80) cc_final: 0.7427 (t80) REVERT: R 809 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8272 (mttt) REVERT: R 822 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6964 (tm-30) outliers start: 22 outliers final: 9 residues processed: 141 average time/residue: 1.4129 time to fit residues: 210.0187 Evaluate side-chains 136 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 628 CYS Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 704 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 31 optimal weight: 0.0570 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8089 Z= 0.151 Angle : 0.493 8.695 10970 Z= 0.257 Chirality : 0.039 0.143 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.023 40.885 1155 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.26 % Allowed : 17.74 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 991 helix: 1.91 (0.28), residues: 371 sheet: -0.24 (0.34), residues: 221 loop : -0.94 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.013 0.001 TYR A 358 ARG 0.009 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7724 (m-30) cc_final: 0.7469 (m-30) REVERT: A 45 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 20 ASP cc_start: 0.8436 (m-30) cc_final: 0.8167 (m-30) REVERT: B 43 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 340 ASN cc_start: 0.7675 (t0) cc_final: 0.7383 (t0) REVERT: G 42 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7490 (tm-30) REVERT: R 650 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7698 (mmp80) REVERT: R 659 GLN cc_start: 0.8364 (mp10) cc_final: 0.8085 (mm-40) REVERT: R 676 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7336 (t-100) REVERT: R 726 TYR cc_start: 0.8087 (t80) cc_final: 0.7463 (t80) REVERT: R 809 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8275 (mttt) REVERT: R 822 GLN cc_start: 0.7496 (tm-30) cc_final: 0.6980 (tm-30) outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 1.3833 time to fit residues: 208.1846 Evaluate side-chains 140 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 628 CYS Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.199 Angle : 0.513 8.969 10970 Z= 0.268 Chirality : 0.040 0.149 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.124 39.893 1155 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.50 % Allowed : 18.93 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 991 helix: 1.88 (0.28), residues: 372 sheet: -0.27 (0.34), residues: 221 loop : -0.95 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE R 832 TYR 0.013 0.001 TYR A 358 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.913 Fit side-chains REVERT: A 43 ASP cc_start: 0.7719 (m-30) cc_final: 0.7455 (m-30) REVERT: A 45 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 20 ASP cc_start: 0.8434 (m-30) cc_final: 0.8161 (m-30) REVERT: B 43 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8714 (mp) REVERT: B 340 ASN cc_start: 0.7692 (t0) cc_final: 0.7440 (t0) REVERT: G 42 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7543 (tm-30) REVERT: R 650 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7663 (mmp80) REVERT: R 659 GLN cc_start: 0.8380 (mp10) cc_final: 0.8087 (mm-40) REVERT: R 676 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7331 (t-100) REVERT: R 726 TYR cc_start: 0.8131 (t80) cc_final: 0.7480 (t80) REVERT: R 809 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8271 (mttt) outliers start: 21 outliers final: 9 residues processed: 145 average time/residue: 1.4428 time to fit residues: 219.6734 Evaluate side-chains 145 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 704 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.187 Angle : 0.537 9.121 10970 Z= 0.275 Chirality : 0.040 0.147 1249 Planarity : 0.004 0.044 1383 Dihedral : 4.080 38.933 1155 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.38 % Allowed : 19.64 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 991 helix: 1.77 (0.28), residues: 378 sheet: -0.31 (0.34), residues: 221 loop : -0.92 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR A 358 ARG 0.011 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.998 Fit side-chains REVERT: A 43 ASP cc_start: 0.7715 (m-30) cc_final: 0.7450 (m-30) REVERT: A 45 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 20 ASP cc_start: 0.8428 (m-30) cc_final: 0.8173 (m-30) REVERT: B 43 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 340 ASN cc_start: 0.7667 (t0) cc_final: 0.7441 (t0) REVERT: G 42 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7588 (tm-30) REVERT: R 650 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7649 (mmp80) REVERT: R 659 GLN cc_start: 0.8370 (mp10) cc_final: 0.8084 (mm-40) REVERT: R 676 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (t-100) REVERT: R 726 TYR cc_start: 0.8123 (t80) cc_final: 0.7476 (t80) REVERT: R 809 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8252 (mttt) outliers start: 20 outliers final: 11 residues processed: 149 average time/residue: 1.5164 time to fit residues: 237.0698 Evaluate side-chains 141 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 82 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.184 Angle : 0.556 11.463 10970 Z= 0.285 Chirality : 0.040 0.145 1249 Planarity : 0.004 0.050 1383 Dihedral : 4.042 37.872 1155 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.38 % Allowed : 20.60 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 991 helix: 1.77 (0.28), residues: 377 sheet: -0.32 (0.34), residues: 221 loop : -0.95 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 832 TYR 0.018 0.001 TYR N 80 ARG 0.013 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7707 (m-30) cc_final: 0.7441 (m-30) REVERT: A 45 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 20 ASP cc_start: 0.8428 (m-30) cc_final: 0.8172 (m-30) REVERT: B 43 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8687 (mp) REVERT: B 340 ASN cc_start: 0.7643 (t0) cc_final: 0.7428 (t0) REVERT: G 42 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7618 (tm-30) REVERT: R 650 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7642 (mmp80) REVERT: R 659 GLN cc_start: 0.8369 (mp10) cc_final: 0.8088 (mm-40) REVERT: R 676 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.7394 (t-100) REVERT: R 726 TYR cc_start: 0.8106 (t80) cc_final: 0.7478 (t80) REVERT: R 809 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8252 (mttt) outliers start: 20 outliers final: 13 residues processed: 136 average time/residue: 1.5113 time to fit residues: 215.5433 Evaluate side-chains 140 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 704 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8089 Z= 0.294 Angle : 0.602 8.767 10970 Z= 0.310 Chirality : 0.042 0.176 1249 Planarity : 0.004 0.047 1383 Dihedral : 4.353 37.329 1155 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 20.95 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 991 helix: 1.77 (0.28), residues: 371 sheet: -0.42 (0.34), residues: 222 loop : -1.00 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 180 TYR 0.018 0.001 TYR N 80 ARG 0.015 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7696 (m-30) cc_final: 0.7413 (m-30) REVERT: A 45 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8183 (tm-30) REVERT: B 20 ASP cc_start: 0.8492 (m-30) cc_final: 0.8249 (m-30) REVERT: B 43 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 340 ASN cc_start: 0.7737 (t0) cc_final: 0.7473 (t0) REVERT: G 42 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7586 (tm-30) REVERT: R 650 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7604 (mmp80) REVERT: R 659 GLN cc_start: 0.8413 (mp10) cc_final: 0.8096 (mm-40) REVERT: R 676 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.7425 (t-100) REVERT: R 809 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8271 (mttt) REVERT: R 825 ARG cc_start: 0.8304 (tmm-80) cc_final: 0.8100 (ttp80) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 1.4735 time to fit residues: 207.2481 Evaluate side-chains 136 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 3 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8089 Z= 0.191 Angle : 0.587 12.451 10970 Z= 0.299 Chirality : 0.040 0.161 1249 Planarity : 0.004 0.054 1383 Dihedral : 4.195 36.868 1155 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.55 % Allowed : 21.43 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 991 helix: 1.90 (0.28), residues: 364 sheet: -0.46 (0.34), residues: 221 loop : -0.93 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE R 832 TYR 0.019 0.001 TYR N 80 ARG 0.013 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7686 (m-30) cc_final: 0.7427 (m-30) REVERT: A 45 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 20 ASP cc_start: 0.8457 (m-30) cc_final: 0.8200 (m-30) REVERT: B 43 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 340 ASN cc_start: 0.7635 (t0) cc_final: 0.7430 (t0) REVERT: G 42 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7543 (tm-30) REVERT: R 650 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7607 (mmp80) REVERT: R 659 GLN cc_start: 0.8364 (mp10) cc_final: 0.8067 (mm-40) REVERT: R 676 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7371 (t-100) REVERT: R 809 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8249 (mttt) REVERT: R 825 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.8083 (ttp80) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 1.4512 time to fit residues: 204.3620 Evaluate side-chains 142 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 71 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 881 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078949 restraints weight = 14730.580| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.62 r_work: 0.3011 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8089 Z= 0.162 Angle : 0.569 8.822 10970 Z= 0.291 Chirality : 0.040 0.157 1249 Planarity : 0.004 0.051 1383 Dihedral : 3.868 35.942 1155 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.79 % Allowed : 21.67 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 991 helix: 1.87 (0.28), residues: 368 sheet: -0.42 (0.34), residues: 224 loop : -0.77 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 36 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE R 856 TYR 0.017 0.001 TYR N 80 ARG 0.013 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.08 seconds wall clock time: 71 minutes 19.97 seconds (4279.97 seconds total)