Starting phenix.real_space_refine on Fri Mar 15 04:20:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijx_35502/03_2024/8ijx_35502_updated.pdb" } resolution = 2.08 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= -0.002 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 1 4.86 5 Be 1 3.05 5 C 6573 2.51 5 N 1654 2.21 5 O 2241 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10545 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7633 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 273 Unusual residues: {' MG': 1, 'PCW': 5, 'PZ0': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 259 Classifications: {'water': 259} Link IDs: {None: 258} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Time building chain proxies: 6.40, per 1000 atoms: 0.61 Number of scatterers: 10545 At special positions: 0 Unit cell: (82.72, 94, 174.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Cl 1 17.00 S 65 16.00 P 6 15.00 Mg 1 11.99 F 3 9.00 O 2241 8.00 N 1654 7.00 C 6573 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " 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 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 43.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.526A pdb=" N GLN A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Processing helix chain 'A' and resid 136 through 170 removed outlier: 4.187A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 292 through 321 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.711A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.523A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 460 through 472 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 543 through 556 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 684 through 693 Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 728 through 736 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 764 through 804 removed outlier: 3.659A pdb=" N LYS A 791 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 4.610A pdb=" N THR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.519A pdb=" N THR A 804 " --> pdb=" O ILE A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 825 through 833 removed outlier: 3.536A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.597A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 956 No H-bonds generated for 'chain 'A' and resid 953 through 956' Processing helix chain 'A' and resid 962 through 980 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 995 through 999 Processing helix chain 'A' and resid 1002 through 1021 Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'B' and resid 34 through 65 Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.589A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 6.733A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing sheet with id= A, first strand: chain 'A' and resid 187 through 190 removed outlier: 11.912A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 236 removed outlier: 4.467A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 260 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS A 258 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.531A pdb=" N ILE A 739 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 623 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET A 697 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.886A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 529 through 532 Processing sheet with id= F, first strand: chain 'A' and resid 211 through 214 removed outlier: 6.407A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 82 through 85 Processing sheet with id= H, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.482A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1155 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: 3.67 Time building geometry restraints manager: 4.91 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: 2686 1.33 - 1.45: 1797 1.45 - 1.57: 5803 1.57 - 1.69: 12 1.69 - 1.81: 98 Bond restraints: 10396 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.765 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.752 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.752 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.446 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 PCW A1105 " pdb=" O3 PCW A1105 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 10391 not shown) Histogram of bond angle deviations from ideal: 85.05 - 94.85: 3 94.85 - 104.65: 217 104.65 - 114.46: 6261 114.46 - 124.26: 7383 124.26 - 134.06: 214 Bond angle restraints: 14078 Sorted by residual: angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 85.05 26.59 3.00e+00 1.11e-01 7.86e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.24 22.87 3.00e+00 1.11e-01 5.81e+01 angle pdb=" C7 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 108.24 86.70 21.54 3.00e+00 1.11e-01 5.16e+01 angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 95.51 17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 118.43 -16.05 3.00e+00 1.11e-01 2.86e+01 ... (remaining 14073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6190 35.81 - 71.63: 169 71.63 - 107.44: 19 107.44 - 143.25: 3 143.25 - 179.07: 2 Dihedral angle restraints: 6383 sinusoidal: 2750 harmonic: 3633 Sorted by residual: dihedral pdb=" CA GLY A 131 " pdb=" C GLY A 131 " pdb=" N ASP A 132 " pdb=" CA ASP A 132 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 53.65 39.35 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" C33 PCW A1104 " pdb=" C31 PCW A1104 " pdb=" C32 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sinusoidal sigma weight residual -168.17 10.90 -179.07 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1290 0.056 - 0.112: 246 0.112 - 0.169: 23 0.169 - 0.225: 5 0.225 - 0.281: 3 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2 PCW A1101 " pdb=" C1 PCW A1101 " pdb=" C3 PCW A1101 " pdb=" O2 PCW A1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C13 CLR B 305 " pdb=" C12 CLR B 305 " pdb=" C14 CLR B 305 " pdb=" C17 CLR B 305 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1564 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.287 2.00e-02 2.50e+03 2.47e-01 7.62e+02 pdb=" C7 NAG B 303 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.008 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.421 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B 302 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.215 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.140 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG B 304 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.023 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 168 2.60 - 3.17: 9033 3.17 - 3.75: 18254 3.75 - 4.32: 25808 4.32 - 4.90: 40022 Nonbonded interactions: 93285 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 2.024 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1225 " model vdw 2.089 2.170 nonbonded pdb=" OD2 ASP A 877 " pdb=" O HOH A1201 " model vdw 2.150 2.440 nonbonded pdb=" F1 BFD A 385 " pdb="MG MG A1102 " model vdw 2.170 2.120 nonbonded pdb=" OE2 GLU A 686 " pdb=" O HOH A1202 " model vdw 2.183 2.440 ... (remaining 93280 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.830 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 32.820 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 0.236 10396 Z= 0.508 Angle : 0.928 26.591 14078 Z= 0.374 Chirality : 0.045 0.281 1567 Planarity : 0.008 0.247 1783 Dihedral : 15.699 179.067 4034 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.50 % Allowed : 6.20 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.40 (0.24), residues: 1244 helix: 1.80 (0.22), residues: 578 sheet: 0.28 (0.40), residues: 153 loop : 0.24 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 915 HIS 0.002 0.001 HIS B 227 PHE 0.017 0.002 PHE B 284 TYR 0.015 0.001 TYR A 802 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8266 (tppt) cc_final: 0.7538 (tmtt) REVERT: A 685 SER cc_start: 0.8093 (m) cc_final: 0.7648 (t) REVERT: B 28 GLN cc_start: 0.6823 (tt0) cc_final: 0.6506 (tt0) REVERT: B 131 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6599 (p) REVERT: B 135 LYS cc_start: 0.7551 (mtpp) cc_final: 0.6757 (tptm) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 1.5505 time to fit residues: 216.0260 Evaluate side-chains 119 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS A 407 HIS B 214 GLN B 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10396 Z= 0.331 Angle : 0.659 7.602 14078 Z= 0.346 Chirality : 0.049 0.248 1567 Planarity : 0.006 0.055 1783 Dihedral : 15.057 173.061 1754 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.35 % Allowed : 7.89 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.07 (0.23), residues: 1244 helix: 1.32 (0.21), residues: 583 sheet: 0.29 (0.39), residues: 161 loop : 0.29 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 915 HIS 0.005 0.002 HIS A 242 PHE 0.022 0.003 PHE B 284 TYR 0.026 0.003 TYR A 802 ARG 0.005 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8269 (tppt) cc_final: 0.7449 (tmtt) REVERT: A 685 SER cc_start: 0.8094 (m) cc_final: 0.7874 (p) REVERT: B 131 CYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6622 (p) REVERT: B 160 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6976 (mm-40) outliers start: 25 outliers final: 15 residues processed: 130 average time/residue: 1.6356 time to fit residues: 226.1347 Evaluate side-chains 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 255 ASN B 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10396 Z= 0.164 Angle : 0.518 6.040 14078 Z= 0.271 Chirality : 0.044 0.251 1567 Planarity : 0.004 0.043 1783 Dihedral : 14.678 168.462 1754 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.88 % Allowed : 9.77 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.25 (0.24), residues: 1244 helix: 1.46 (0.21), residues: 583 sheet: 0.43 (0.39), residues: 166 loop : 0.37 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 970 TYR 0.014 0.001 TYR A 802 ARG 0.004 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8251 (tppt) cc_final: 0.7496 (tmtt) REVERT: A 462 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: A 685 SER cc_start: 0.8079 (m) cc_final: 0.7872 (p) REVERT: B 131 CYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6588 (p) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 1.6059 time to fit residues: 211.8468 Evaluate side-chains 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10396 Z= 0.235 Angle : 0.572 6.571 14078 Z= 0.299 Chirality : 0.046 0.239 1567 Planarity : 0.005 0.046 1783 Dihedral : 14.732 170.001 1753 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.35 % Allowed : 9.49 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.13 (0.23), residues: 1244 helix: 1.35 (0.21), residues: 582 sheet: 0.28 (0.38), residues: 171 loop : 0.37 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 915 HIS 0.004 0.001 HIS B 227 PHE 0.016 0.002 PHE B 284 TYR 0.018 0.002 TYR A 802 ARG 0.004 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 685 SER cc_start: 0.8060 (m) cc_final: 0.7818 (p) REVERT: B 131 CYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6532 (p) outliers start: 25 outliers final: 16 residues processed: 127 average time/residue: 1.5517 time to fit residues: 210.0360 Evaluate side-chains 124 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10396 Z= 0.195 Angle : 0.537 6.308 14078 Z= 0.281 Chirality : 0.044 0.242 1567 Planarity : 0.005 0.041 1783 Dihedral : 14.612 176.463 1751 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.69 % Allowed : 11.00 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.20 (0.23), residues: 1244 helix: 1.40 (0.21), residues: 581 sheet: 0.30 (0.38), residues: 171 loop : 0.41 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.003 0.001 HIS A 629 PHE 0.013 0.002 PHE B 284 TYR 0.016 0.002 TYR A 802 ARG 0.005 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.7865 (m) cc_final: 0.7662 (t) REVERT: B 131 CYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6421 (p) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 1.5795 time to fit residues: 199.8803 Evaluate side-chains 120 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10396 Z= 0.235 Angle : 0.571 6.559 14078 Z= 0.299 Chirality : 0.046 0.239 1567 Planarity : 0.005 0.040 1783 Dihedral : 14.718 176.911 1751 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.07 % Allowed : 10.81 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.11 (0.23), residues: 1244 helix: 1.32 (0.21), residues: 581 sheet: 0.24 (0.38), residues: 171 loop : 0.39 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 915 HIS 0.004 0.001 HIS B 227 PHE 0.015 0.002 PHE B 284 TYR 0.018 0.002 TYR A 802 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.7882 (m) cc_final: 0.7678 (t) REVERT: B 131 CYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6563 (p) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 1.5437 time to fit residues: 210.2575 Evaluate side-chains 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10396 Z= 0.151 Angle : 0.500 5.670 14078 Z= 0.261 Chirality : 0.043 0.253 1567 Planarity : 0.004 0.036 1783 Dihedral : 14.278 172.175 1751 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 11.65 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.25 (0.24), residues: 1244 helix: 1.48 (0.22), residues: 581 sheet: 0.33 (0.38), residues: 171 loop : 0.39 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.004 0.001 HIS A 407 PHE 0.014 0.001 PHE A 970 TYR 0.012 0.001 TYR A 802 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.7849 (mmp-170) cc_final: 0.7561 (mmm160) REVERT: A 462 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: A 477 MET cc_start: 0.6750 (mmt) cc_final: 0.6331 (mpt) REVERT: B 131 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6230 (p) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 1.5859 time to fit residues: 204.0747 Evaluate side-chains 122 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 108 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10396 Z= 0.182 Angle : 0.527 6.160 14078 Z= 0.276 Chirality : 0.044 0.244 1567 Planarity : 0.004 0.037 1783 Dihedral : 14.149 170.272 1751 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.26 % Allowed : 11.28 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.23 (0.23), residues: 1244 helix: 1.45 (0.22), residues: 576 sheet: 0.34 (0.38), residues: 171 loop : 0.39 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 PHE 0.016 0.002 PHE A 970 TYR 0.015 0.002 TYR A 802 ARG 0.005 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.5066 (OUTLIER) cc_final: 0.4194 (tt0) REVERT: A 462 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 477 MET cc_start: 0.6733 (mmt) cc_final: 0.6355 (mpt) REVERT: A 498 GLN cc_start: 0.8342 (tt0) cc_final: 0.7935 (tt0) REVERT: B 115 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.7312 (mmp-170) outliers start: 24 outliers final: 19 residues processed: 128 average time/residue: 1.6096 time to fit residues: 219.1910 Evaluate side-chains 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10396 Z= 0.179 Angle : 0.525 6.069 14078 Z= 0.275 Chirality : 0.044 0.245 1567 Planarity : 0.004 0.037 1783 Dihedral : 14.018 169.676 1751 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.16 % Allowed : 11.00 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.23 (0.23), residues: 1244 helix: 1.44 (0.22), residues: 576 sheet: 0.37 (0.38), residues: 171 loop : 0.39 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 PHE 0.015 0.002 PHE A 970 TYR 0.015 0.002 TYR B 43 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.5019 (OUTLIER) cc_final: 0.4161 (tt0) REVERT: A 462 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 477 MET cc_start: 0.6724 (mmt) cc_final: 0.6369 (mpt) REVERT: A 498 GLN cc_start: 0.8324 (tt0) cc_final: 0.7995 (tt0) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 1.6360 time to fit residues: 219.4137 Evaluate side-chains 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10396 Z= 0.209 Angle : 0.550 6.368 14078 Z= 0.288 Chirality : 0.045 0.240 1567 Planarity : 0.005 0.038 1783 Dihedral : 14.101 170.131 1751 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.07 % Allowed : 11.18 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.18 (0.23), residues: 1244 helix: 1.40 (0.21), residues: 575 sheet: 0.33 (0.38), residues: 171 loop : 0.37 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 915 HIS 0.004 0.001 HIS B 227 PHE 0.017 0.002 PHE A 970 TYR 0.016 0.002 TYR B 43 ARG 0.006 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.154 Fit side-chains REVERT: A 176 GLN cc_start: 0.4992 (OUTLIER) cc_final: 0.4095 (tt0) REVERT: A 462 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: A 477 MET cc_start: 0.6730 (mmt) cc_final: 0.6399 (mpt) REVERT: A 498 GLN cc_start: 0.8354 (tt0) cc_final: 0.7978 (tt0) REVERT: A 956 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7449 (tt0) outliers start: 22 outliers final: 19 residues processed: 124 average time/residue: 1.5768 time to fit residues: 207.9687 Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123097 restraints weight = 8494.996| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.40 r_work: 0.3189 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10396 Z= 0.301 Angle : 0.629 6.979 14078 Z= 0.330 Chirality : 0.048 0.227 1567 Planarity : 0.005 0.050 1783 Dihedral : 14.543 172.794 1751 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.07 % Allowed : 11.28 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.02 (0.23), residues: 1244 helix: 1.24 (0.21), residues: 574 sheet: 0.24 (0.38), residues: 171 loop : 0.34 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 39 HIS 0.006 0.001 HIS B 227 PHE 0.018 0.002 PHE B 284 TYR 0.019 0.003 TYR B 43 ARG 0.006 0.001 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.81 seconds wall clock time: 79 minutes 51.44 seconds (4791.44 seconds total)