Starting phenix.real_space_refine on Sat Apr 6 09:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/04_2024/7wu2_32817.pdb" } resolution = 2.8 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 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 4968 2.51 5 N 1361 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2115 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 269} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.51, per 1000 atoms: 0.58 Number of scatterers: 7829 At special positions: 0 Unit cell: (106.029, 118.881, 83.538, 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 1450 8.00 N 1361 7.00 C 4968 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=2.02 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 40.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.904A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.675A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.196A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.860A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.613A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.733A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.305A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.503A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 559 through 591 Processing helix chain 'R' and resid 592 through 594 No H-bonds generated for 'chain 'R' and resid 592 through 594' Processing helix chain 'R' and resid 601 through 623 Processing helix chain 'R' and resid 629 through 662 removed outlier: 4.006A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 646 " --> pdb=" O PHE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 680 Processing helix chain 'R' and resid 680 through 694 removed outlier: 3.706A pdb=" N LEU R 684 " --> pdb=" O TRP R 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 737 Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 738 through 745 Processing helix chain 'R' and resid 745 through 750 removed outlier: 4.002A pdb=" N HIS R 749 " --> pdb=" O ASN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 752 through 764 removed outlier: 3.967A pdb=" N LYS R 756 " --> pdb=" O PRO R 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 757 " --> pdb=" O SER R 753 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 758 " --> pdb=" O ALA R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 770 removed outlier: 4.572A pdb=" N ILE R 768 " --> pdb=" O VAL R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 778 removed outlier: 3.822A pdb=" N VAL R 777 " --> pdb=" O TRP R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 779 through 781 No H-bonds generated for 'chain 'R' and resid 779 through 781' Processing helix chain 'R' and resid 783 through 797 removed outlier: 3.647A pdb=" N PHE R 787 " --> pdb=" O CYS R 783 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 807 Processing helix chain 'R' and resid 810 through 821 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.251A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.759A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.714A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.393A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.046A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 2.32 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2552 1.34 - 1.46: 1364 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 7992 Sorted by residual: bond pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.23e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" N TYR A 253 " pdb=" CA TYR A 253 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.84e+00 bond pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.02e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.71: 110 105.71 - 112.80: 4282 112.80 - 119.90: 2627 119.90 - 126.99: 3735 126.99 - 134.09: 91 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASP A 49 " pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CB ARG B 8 " pdb=" CG ARG B 8 " pdb=" CD ARG B 8 " ideal model delta sigma weight residual 111.30 119.21 -7.91 2.30e+00 1.89e-01 1.18e+01 angle pdb=" C ASN R 546 " pdb=" N PHE R 547 " pdb=" CA PHE R 547 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.28 114.62 -4.34 1.55e+00 4.16e-01 7.84e+00 angle pdb=" N ASN A 50 " pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 110.49 115.04 -4.55 1.69e+00 3.50e-01 7.25e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4345 17.88 - 35.75: 321 35.75 - 53.63: 47 53.63 - 71.51: 9 71.51 - 89.38: 7 Dihedral angle restraints: 4729 sinusoidal: 1800 harmonic: 2929 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual -86.00 -132.06 46.06 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.57 -43.43 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 876 0.037 - 0.075: 263 0.075 - 0.112: 73 0.112 - 0.149: 22 0.149 - 0.186: 2 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA THR R 630 " pdb=" N THR R 630 " pdb=" C THR R 630 " pdb=" CB THR R 630 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1233 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ASP A 49 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 50 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASP A 252 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 252 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 253 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 598 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG R 598 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG R 598 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN R 599 " 0.008 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 7936 3.28 - 3.82: 13282 3.82 - 4.36: 15829 4.36 - 4.90: 27202 Nonbonded interactions: 64765 Sorted by model distance: nonbonded pdb=" O THR R 596 " pdb=" ND2 ASN R 599 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.217 2.440 nonbonded pdb=" O ASP R 696 " pdb=" OG1 THR R 700 " model vdw 2.262 2.440 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.307 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.314 2.440 ... (remaining 64760 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.000 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.002 0.031 7992 Z= 0.130 Angle : 0.513 9.441 10845 Z= 0.275 Chirality : 0.041 0.186 1236 Planarity : 0.003 0.040 1385 Dihedral : 12.858 89.384 2828 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 0.79 (0.27), residues: 998 helix: 1.38 (0.29), residues: 369 sheet: 0.65 (0.34), residues: 224 loop : -0.27 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.009 0.001 HIS B 266 PHE 0.010 0.001 PHE N 29 TYR 0.013 0.001 TYR R 789 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.849 Fit side-chains REVERT: A 55 THR cc_start: 0.7759 (m) cc_final: 0.7467 (p) REVERT: A 307 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7655 (mmmt) REVERT: A 343 ASP cc_start: 0.6462 (m-30) cc_final: 0.6038 (m-30) REVERT: R 804 LEU cc_start: 0.8517 (tt) cc_final: 0.8243 (tp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.1264 time to fit residues: 185.9316 Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 32 GLN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7992 Z= 0.254 Angle : 0.566 7.890 10845 Z= 0.301 Chirality : 0.043 0.150 1236 Planarity : 0.004 0.046 1385 Dihedral : 4.267 27.781 1095 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.70 % Allowed : 10.02 % Favored : 86.28 % 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: 1.14 (0.27), residues: 998 helix: 2.00 (0.29), residues: 357 sheet: 0.49 (0.34), residues: 221 loop : -0.12 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.010 0.002 HIS A 357 PHE 0.015 0.002 PHE R 665 TYR 0.023 0.002 TYR B 59 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.966 Fit side-chains REVERT: A 314 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 156 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: B 325 MET cc_start: 0.7867 (tpt) cc_final: 0.7658 (mmt) REVERT: N 31 ASN cc_start: 0.8149 (m-40) cc_final: 0.7772 (m-40) outliers start: 31 outliers final: 13 residues processed: 134 average time/residue: 1.0114 time to fit residues: 145.3960 Evaluate side-chains 130 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 700 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 278 ASN B 32 GLN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 562 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7992 Z= 0.265 Angle : 0.555 9.536 10845 Z= 0.296 Chirality : 0.043 0.171 1236 Planarity : 0.004 0.046 1385 Dihedral : 4.380 32.074 1095 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.89 % Allowed : 13.37 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.95 (0.27), residues: 998 helix: 1.87 (0.28), residues: 363 sheet: 0.41 (0.34), residues: 216 loop : -0.29 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.010 0.002 PHE A 208 TYR 0.016 0.002 TYR A 391 ARG 0.003 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 0.854 Fit side-chains REVERT: B 156 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: B 325 MET cc_start: 0.7884 (tpt) cc_final: 0.7592 (mmt) REVERT: N 31 ASN cc_start: 0.8424 (m-40) cc_final: 0.8130 (m110) REVERT: N 43 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6777 (mmtp) REVERT: N 77 ASN cc_start: 0.7798 (m-40) cc_final: 0.7540 (m-40) REVERT: R 635 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.5945 (ppp) outliers start: 41 outliers final: 22 residues processed: 137 average time/residue: 1.0788 time to fit residues: 158.1571 Evaluate side-chains 129 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 788 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 chunk 84 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7992 Z= 0.179 Angle : 0.493 8.369 10845 Z= 0.263 Chirality : 0.041 0.146 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.141 31.150 1095 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.30 % Allowed : 16.11 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.00 (0.27), residues: 998 helix: 2.05 (0.28), residues: 362 sheet: 0.38 (0.34), residues: 220 loop : -0.37 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.010 0.001 TYR N 95 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.857 Fit side-chains REVERT: A 309 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: B 325 MET cc_start: 0.7885 (tpt) cc_final: 0.7665 (mmt) REVERT: N 43 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6793 (mmtp) REVERT: N 77 ASN cc_start: 0.7789 (m-40) cc_final: 0.7572 (m-40) outliers start: 36 outliers final: 19 residues processed: 125 average time/residue: 1.0465 time to fit residues: 140.3623 Evaluate side-chains 121 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 703 ASN Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS R 788 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7992 Z= 0.183 Angle : 0.499 8.996 10845 Z= 0.265 Chirality : 0.041 0.144 1236 Planarity : 0.003 0.038 1385 Dihedral : 4.125 30.782 1095 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.18 % Allowed : 17.66 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.00 (0.27), residues: 998 helix: 2.08 (0.28), residues: 362 sheet: 0.42 (0.34), residues: 214 loop : -0.43 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.854 Fit side-chains REVERT: B 325 MET cc_start: 0.7795 (tpt) cc_final: 0.7579 (mmt) REVERT: N 43 LYS cc_start: 0.7263 (mtpp) cc_final: 0.6818 (mmtp) REVERT: N 77 ASN cc_start: 0.7771 (m-40) cc_final: 0.7553 (m-40) REVERT: R 558 LEU cc_start: 0.6464 (mt) cc_final: 0.6243 (mt) REVERT: R 695 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5502 (ttm) outliers start: 35 outliers final: 20 residues processed: 132 average time/residue: 1.0886 time to fit residues: 154.2439 Evaluate side-chains 125 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS R 600 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7992 Z= 0.362 Angle : 0.619 10.459 10845 Z= 0.329 Chirality : 0.045 0.165 1236 Planarity : 0.004 0.060 1385 Dihedral : 4.722 36.293 1095 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 4.77 % Allowed : 18.14 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.63 (0.26), residues: 998 helix: 1.68 (0.27), residues: 362 sheet: 0.30 (0.34), residues: 214 loop : -0.58 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.014 0.002 PHE A 208 TYR 0.017 0.002 TYR N 95 ARG 0.004 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 0.834 Fit side-chains REVERT: A 314 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: B 325 MET cc_start: 0.7824 (tpt) cc_final: 0.7597 (mmt) REVERT: N 89 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: R 735 THR cc_start: 0.7812 (m) cc_final: 0.7564 (p) outliers start: 40 outliers final: 26 residues processed: 126 average time/residue: 1.1223 time to fit residues: 150.9513 Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7992 Z= 0.198 Angle : 0.506 7.946 10845 Z= 0.271 Chirality : 0.041 0.155 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.347 36.128 1095 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.46 % Allowed : 19.33 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.77 (0.27), residues: 998 helix: 1.90 (0.27), residues: 362 sheet: 0.23 (0.34), residues: 215 loop : -0.52 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.752 Fit side-chains REVERT: A 232 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8272 (ttm170) REVERT: B 75 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8218 (mm110) REVERT: B 325 MET cc_start: 0.7808 (tpt) cc_final: 0.7500 (mmt) REVERT: N 43 LYS cc_start: 0.7410 (mtpp) cc_final: 0.6924 (mmtp) REVERT: R 695 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5251 (ttm) REVERT: R 735 THR cc_start: 0.7936 (m) cc_final: 0.7678 (p) outliers start: 29 outliers final: 19 residues processed: 126 average time/residue: 1.1470 time to fit residues: 153.9520 Evaluate side-chains 123 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS B 340 ASN C 59 ASN R 562 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7992 Z= 0.370 Angle : 0.620 10.050 10845 Z= 0.329 Chirality : 0.045 0.169 1236 Planarity : 0.004 0.057 1385 Dihedral : 4.747 38.312 1095 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 4.18 % Allowed : 19.81 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.52 (0.26), residues: 998 helix: 1.57 (0.27), residues: 362 sheet: 0.22 (0.33), residues: 222 loop : -0.63 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.002 PHE A 208 TYR 0.017 0.002 TYR N 95 ARG 0.005 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 0.831 Fit side-chains REVERT: A 38 ARG cc_start: 0.8311 (mmt180) cc_final: 0.8042 (mmt90) REVERT: A 232 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8366 (ttm170) REVERT: A 314 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: B 10 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: B 46 ARG cc_start: 0.7160 (mpt180) cc_final: 0.6847 (mmt-90) REVERT: B 325 MET cc_start: 0.7829 (tpt) cc_final: 0.7598 (mmt) REVERT: N 43 LYS cc_start: 0.7468 (mtpp) cc_final: 0.6963 (mmtp) REVERT: N 89 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: R 735 THR cc_start: 0.7876 (m) cc_final: 0.7633 (p) outliers start: 35 outliers final: 25 residues processed: 122 average time/residue: 1.1112 time to fit residues: 144.7114 Evaluate side-chains 125 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS ** R 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7992 Z= 0.155 Angle : 0.488 7.651 10845 Z= 0.259 Chirality : 0.040 0.145 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.210 36.452 1095 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.74 % Allowed : 21.84 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.86 (0.27), residues: 998 helix: 2.00 (0.28), residues: 362 sheet: 0.33 (0.34), residues: 214 loop : -0.53 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.008 0.001 TYR R 602 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.914 Fit side-chains REVERT: A 232 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: B 75 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8182 (mm110) REVERT: B 325 MET cc_start: 0.7808 (tpt) cc_final: 0.7580 (mmt) REVERT: N 43 LYS cc_start: 0.7332 (mtpp) cc_final: 0.6880 (mmtp) REVERT: R 735 THR cc_start: 0.7957 (m) cc_final: 0.7714 (p) outliers start: 23 outliers final: 18 residues processed: 121 average time/residue: 1.1596 time to fit residues: 149.6086 Evaluate side-chains 119 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7992 Z= 0.230 Angle : 0.536 8.193 10845 Z= 0.284 Chirality : 0.042 0.157 1236 Planarity : 0.004 0.037 1385 Dihedral : 4.336 36.376 1095 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.86 % Allowed : 22.08 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.82 (0.27), residues: 998 helix: 1.93 (0.27), residues: 362 sheet: 0.30 (0.34), residues: 214 loop : -0.52 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.002 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.892 Fit side-chains REVERT: A 232 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8348 (ttm170) REVERT: B 75 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (mm110) REVERT: N 43 LYS cc_start: 0.7383 (mtpp) cc_final: 0.6950 (mmtp) REVERT: R 735 THR cc_start: 0.7981 (m) cc_final: 0.7755 (p) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 1.1300 time to fit residues: 141.0481 Evaluate side-chains 117 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN B 266 HIS R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127865 restraints weight = 8015.365| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3301 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7992 Z= 0.181 Angle : 0.501 7.577 10845 Z= 0.266 Chirality : 0.040 0.149 1236 Planarity : 0.003 0.036 1385 Dihedral : 4.187 35.826 1095 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.63 % Allowed : 22.43 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.90 (0.27), residues: 998 helix: 2.05 (0.28), residues: 362 sheet: 0.28 (0.34), residues: 214 loop : -0.49 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.56 seconds wall clock time: 57 minutes 35.17 seconds (3455.17 seconds total)