Starting phenix.real_space_refine on Thu Feb 15 19:34:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuq_32838/02_2024/7wuq_32838.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5293 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5090 2.51 5 N 1383 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 609": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1795 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2564 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 421 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2226 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 4.65, per 1000 atoms: 0.58 Number of scatterers: 7973 At special positions: 0 Unit cell: (93, 113, 87, 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 49 16.00 O 1451 8.00 N 1383 7.00 C 5090 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=2.61 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.39 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.20 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 39.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.841A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.014A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.541A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.564A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.201A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.703A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.506A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.674A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.545A pdb=" N ALA N 56 " --> pdb=" O GLN N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'R' and resid 600 through 605 removed outlier: 3.532A pdb=" N ILE R 603 " --> pdb=" O SER R 600 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 645 removed outlier: 3.703A pdb=" N MET R 618 " --> pdb=" O PRO R 614 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 619 " --> pdb=" O SER R 615 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU R 630 " --> pdb=" O ILE R 626 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA R 644 " --> pdb=" O VAL R 640 " (cutoff:3.500A) Processing helix chain 'R' and resid 646 through 649 Processing helix chain 'R' and resid 651 through 676 removed outlier: 3.690A pdb=" N LYS R 655 " --> pdb=" O ASP R 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP R 674 " --> pdb=" O ILE R 670 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 716 removed outlier: 3.585A pdb=" N MET R 704 " --> pdb=" O SER R 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU R 707 " --> pdb=" O TRP R 703 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 716 " --> pdb=" O TYR R 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 725 through 735 removed outlier: 3.626A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 735 through 749 Processing helix chain 'R' and resid 750 through 753 removed outlier: 4.184A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 774 through 782 Processing helix chain 'R' and resid 782 through 795 removed outlier: 3.839A pdb=" N LEU R 792 " --> pdb=" O VAL R 788 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 810 removed outlier: 4.303A pdb=" N ILE R 807 " --> pdb=" O GLN R 803 " (cutoff:3.500A) Processing helix chain 'R' and resid 820 through 835 Processing helix chain 'R' and resid 836 through 842 removed outlier: 3.577A pdb=" N ALA R 841 " --> pdb=" O TRP R 838 " (cutoff:3.500A) Processing helix chain 'R' and resid 848 through 860 removed outlier: 3.509A pdb=" N MET R 853 " --> pdb=" O ASN R 849 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR R 854 " --> pdb=" O VAL R 850 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 885 removed outlier: 3.616A pdb=" N GLN R 881 " --> pdb=" O ASN R 877 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP R 882 " --> pdb=" O VAL R 878 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG R 883 " --> pdb=" O ARG R 879 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG R 884 " --> pdb=" O LYS R 880 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.533A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.662A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113 removed outlier: 6.284A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.568A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.009A 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: 6.696A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.327A 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: 6.970A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.574A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.696A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.549A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1020 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: 2.60 Time building geometry restraints manager: 3.30 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: 2448 1.34 - 1.46: 1823 1.46 - 1.58: 3797 1.58 - 1.70: 1 1.70 - 1.82: 68 Bond restraints: 8137 Sorted by residual: bond pdb=" CA ARG A 356 " pdb=" CB ARG A 356 " ideal model delta sigma weight residual 1.526 1.616 -0.090 1.76e-02 3.23e+03 2.59e+01 bond pdb=" CA CYS B 317 " pdb=" C CYS B 317 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.04e-02 9.25e+03 4.84e+00 bond pdb=" CA CYS B 103 " pdb=" C CYS B 103 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.34e-02 5.57e+03 4.71e+00 bond pdb=" CB THR B 243 " pdb=" CG2 THR B 243 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" N ALA B 104 " pdb=" CA ALA B 104 " ideal model delta sigma weight residual 1.456 1.434 0.023 1.21e-02 6.83e+03 3.57e+00 ... (remaining 8132 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.17: 76 104.17 - 111.69: 3472 111.69 - 119.22: 3122 119.22 - 126.75: 4239 126.75 - 134.28: 104 Bond angle restraints: 11013 Sorted by residual: angle pdb=" N ARG R 683 " pdb=" CA ARG R 683 " pdb=" C ARG R 683 " ideal model delta sigma weight residual 111.28 118.02 -6.74 1.09e+00 8.42e-01 3.82e+01 angle pdb=" N THR A 40 " pdb=" CA THR A 40 " pdb=" C THR A 40 " ideal model delta sigma weight residual 111.36 117.34 -5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" C ALA R 844 " pdb=" N TRP R 845 " pdb=" CA TRP R 845 " ideal model delta sigma weight residual 121.70 130.52 -8.82 1.80e+00 3.09e-01 2.40e+01 angle pdb=" CB MET N 34 " pdb=" CG MET N 34 " pdb=" SD MET N 34 " ideal model delta sigma weight residual 112.70 126.93 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" N SER R 608 " pdb=" CA SER R 608 " pdb=" C SER R 608 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4357 17.82 - 35.64: 372 35.64 - 53.46: 70 53.46 - 71.28: 14 71.28 - 89.10: 8 Dihedral angle restraints: 4821 sinusoidal: 1893 harmonic: 2928 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N LYS A 34 " pdb=" CA LYS A 34 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 4818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1079 0.093 - 0.185: 149 0.185 - 0.278: 11 0.278 - 0.370: 3 0.370 - 0.463: 2 Chirality restraints: 1244 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA TRP R 845 " pdb=" N TRP R 845 " pdb=" C TRP R 845 " pdb=" CB TRP R 845 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1241 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 652 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 653 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 653 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 653 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " -0.299 9.50e-02 1.11e+02 1.34e-01 1.23e+01 pdb=" NE ARG B 314 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 844 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ALA R 844 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA R 844 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP R 845 " -0.020 2.00e-02 2.50e+03 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 737 2.74 - 3.28: 8129 3.28 - 3.82: 14543 3.82 - 4.36: 17975 4.36 - 4.90: 29326 Nonbonded interactions: 70710 Sorted by model distance: nonbonded pdb=" O TRP R 845 " pdb=" N ASN R 849 " model vdw 2.204 2.520 nonbonded pdb=" O GLY R 754 " pdb=" ND2 ASN R 773 " model vdw 2.240 2.520 nonbonded pdb=" C TRP R 845 " pdb=" CD PRO R 847 " model vdw 2.248 3.670 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.256 2.440 nonbonded pdb=" O GLY R 754 " pdb=" OD1 ASN R 773 " model vdw 2.267 3.040 ... (remaining 70705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 2.020 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.600 Find NCS groups from input model: 0.210 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8137 Z= 0.381 Angle : 1.061 14.234 11013 Z= 0.595 Chirality : 0.066 0.463 1244 Planarity : 0.009 0.134 1394 Dihedral : 14.173 89.100 2918 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.47 % Allowed : 1.87 % Favored : 97.67 % Cbeta Deviations : 0.11 % 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: -3.00 (0.24), residues: 987 helix: -2.27 (0.21), residues: 347 sheet: -2.06 (0.38), residues: 157 loop : -1.62 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 339 HIS 0.021 0.004 HIS A 357 PHE 0.038 0.003 PHE R 730 TYR 0.021 0.002 TYR N 115 ARG 0.020 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 VAL cc_start: 0.4845 (p) cc_final: 0.4604 (p) REVERT: B 314 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7646 (ptm160) REVERT: G 38 MET cc_start: 0.5765 (mtp) cc_final: 0.5322 (mtm) REVERT: R 646 GLU cc_start: 0.7088 (tp30) cc_final: 0.6817 (tp30) outliers start: 4 outliers final: 1 residues processed: 181 average time/residue: 0.7792 time to fit residues: 153.6174 Evaluate side-chains 143 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 618 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 668 ASN R 849 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8137 Z= 0.256 Angle : 0.612 7.357 11013 Z= 0.329 Chirality : 0.043 0.144 1244 Planarity : 0.005 0.069 1394 Dihedral : 5.351 24.405 1102 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 11.44 % Favored : 86.46 % 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: -1.67 (0.25), residues: 987 helix: -0.28 (0.26), residues: 346 sheet: -1.95 (0.36), residues: 178 loop : -1.29 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 730 TYR 0.012 0.002 TYR R 726 ARG 0.005 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 THR cc_start: 0.7561 (t) cc_final: 0.7357 (p) REVERT: B 318 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (pp) outliers start: 18 outliers final: 8 residues processed: 193 average time/residue: 0.8671 time to fit residues: 180.8870 Evaluate side-chains 169 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 792 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN R 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8137 Z= 0.217 Angle : 0.579 7.821 11013 Z= 0.303 Chirality : 0.042 0.134 1244 Planarity : 0.004 0.059 1394 Dihedral : 4.972 21.805 1099 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.80 % Allowed : 16.45 % Favored : 80.75 % 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: -1.05 (0.26), residues: 987 helix: 0.53 (0.27), residues: 338 sheet: -1.82 (0.36), residues: 189 loop : -1.04 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.002 PHE R 730 TYR 0.015 0.001 TYR R 753 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6442 (tp30) cc_final: 0.6208 (tt0) REVERT: B 78 LYS cc_start: 0.8116 (tppp) cc_final: 0.7691 (tppt) REVERT: B 155 ASN cc_start: 0.7277 (t0) cc_final: 0.7030 (t0) REVERT: B 171 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6124 (mp) REVERT: B 325 MET cc_start: 0.5714 (mmp) cc_final: 0.4482 (mmp) REVERT: R 646 GLU cc_start: 0.7380 (tt0) cc_final: 0.6804 (tp30) outliers start: 24 outliers final: 10 residues processed: 192 average time/residue: 0.8698 time to fit residues: 180.8441 Evaluate side-chains 169 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 598 LEU Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 803 GLN R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8137 Z= 0.246 Angle : 0.576 7.508 11013 Z= 0.302 Chirality : 0.041 0.138 1244 Planarity : 0.004 0.053 1394 Dihedral : 4.927 21.214 1099 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.27 % Allowed : 19.02 % Favored : 77.71 % 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: -0.86 (0.26), residues: 987 helix: 0.86 (0.27), residues: 342 sheet: -1.88 (0.35), residues: 186 loop : -1.02 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.011 0.002 HIS A 357 PHE 0.014 0.002 PHE R 601 TYR 0.010 0.001 TYR A 358 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6476 (tp30) cc_final: 0.6147 (tt0) REVERT: B 155 ASN cc_start: 0.7278 (t0) cc_final: 0.6967 (t0) REVERT: B 171 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6413 (mp) REVERT: B 325 MET cc_start: 0.6147 (mmp) cc_final: 0.4893 (mmp) REVERT: R 753 TYR cc_start: 0.8560 (m-80) cc_final: 0.7880 (m-80) outliers start: 28 outliers final: 14 residues processed: 199 average time/residue: 0.8137 time to fit residues: 176.3598 Evaluate side-chains 184 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.0000 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.0970 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 773 ASN R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8137 Z= 0.194 Angle : 0.561 10.363 11013 Z= 0.290 Chirality : 0.041 0.203 1244 Planarity : 0.004 0.046 1394 Dihedral : 4.742 20.796 1099 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.50 % Allowed : 19.95 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 987 helix: 1.10 (0.28), residues: 341 sheet: -2.00 (0.34), residues: 208 loop : -0.86 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR R 785 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6202 (tp30) cc_final: 0.5937 (tt0) REVERT: B 155 ASN cc_start: 0.6998 (t0) cc_final: 0.6522 (p0) REVERT: B 171 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6450 (mp) REVERT: B 325 MET cc_start: 0.6019 (mmp) cc_final: 0.4756 (mmp) REVERT: N 20 LEU cc_start: 0.8015 (mt) cc_final: 0.7630 (mt) REVERT: R 711 MET cc_start: 0.7925 (mtt) cc_final: 0.7579 (mtt) outliers start: 30 outliers final: 16 residues processed: 194 average time/residue: 0.7740 time to fit residues: 164.3043 Evaluate side-chains 187 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8137 Z= 0.206 Angle : 0.573 7.842 11013 Z= 0.294 Chirality : 0.041 0.138 1244 Planarity : 0.004 0.043 1394 Dihedral : 4.681 20.491 1099 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.73 % Allowed : 20.65 % Favored : 75.61 % 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: -0.66 (0.27), residues: 987 helix: 1.22 (0.28), residues: 341 sheet: -1.97 (0.34), residues: 206 loop : -0.90 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.001 PHE R 852 TYR 0.012 0.001 TYR A 358 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6252 (tp30) cc_final: 0.6003 (tt0) REVERT: B 171 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6503 (mp) REVERT: B 325 MET cc_start: 0.6090 (mmp) cc_final: 0.4806 (mmp) REVERT: R 711 MET cc_start: 0.7895 (mtt) cc_final: 0.7600 (mtt) REVERT: R 753 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: R 832 PHE cc_start: 0.8223 (m-80) cc_final: 0.8010 (m-80) outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 0.7324 time to fit residues: 150.5319 Evaluate side-chains 182 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 799 VAL Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 57 optimal weight: 0.0020 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8137 Z= 0.192 Angle : 0.560 7.771 11013 Z= 0.288 Chirality : 0.041 0.204 1244 Planarity : 0.004 0.043 1394 Dihedral : 4.606 19.995 1099 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.73 % Allowed : 21.59 % Favored : 74.68 % 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: -0.60 (0.27), residues: 987 helix: 1.31 (0.28), residues: 340 sheet: -1.96 (0.34), residues: 206 loop : -0.88 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.013 0.001 TYR R 785 ARG 0.012 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6175 (tp30) cc_final: 0.5942 (tt0) REVERT: B 171 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6142 (mp) REVERT: B 325 MET cc_start: 0.5961 (mmp) cc_final: 0.4628 (mmp) REVERT: N 31 ASN cc_start: 0.7965 (m-40) cc_final: 0.7720 (m110) REVERT: R 711 MET cc_start: 0.7869 (mtt) cc_final: 0.7584 (mtt) REVERT: R 753 TYR cc_start: 0.8594 (m-80) cc_final: 0.8034 (m-80) outliers start: 32 outliers final: 19 residues processed: 187 average time/residue: 0.7443 time to fit residues: 152.7416 Evaluate side-chains 185 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8137 Z= 0.218 Angle : 0.579 11.705 11013 Z= 0.296 Chirality : 0.041 0.139 1244 Planarity : 0.004 0.054 1394 Dihedral : 4.640 19.508 1099 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.80 % Allowed : 23.34 % Favored : 73.86 % 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: -0.61 (0.27), residues: 987 helix: 1.30 (0.28), residues: 340 sheet: -2.01 (0.33), residues: 212 loop : -0.83 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.021 0.001 PHE R 601 TYR 0.010 0.001 TYR A 358 ARG 0.013 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6212 (tp30) cc_final: 0.5976 (tt0) REVERT: B 171 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6197 (mp) REVERT: B 325 MET cc_start: 0.5923 (mmp) cc_final: 0.4606 (mmp) REVERT: N 31 ASN cc_start: 0.7894 (m-40) cc_final: 0.7682 (m110) REVERT: R 753 TYR cc_start: 0.8651 (m-80) cc_final: 0.8035 (m-80) REVERT: R 832 PHE cc_start: 0.8220 (m-80) cc_final: 0.8014 (m-80) outliers start: 24 outliers final: 17 residues processed: 181 average time/residue: 0.7273 time to fit residues: 144.6480 Evaluate side-chains 173 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8137 Z= 0.188 Angle : 0.572 9.588 11013 Z= 0.293 Chirality : 0.041 0.186 1244 Planarity : 0.004 0.060 1394 Dihedral : 4.551 18.972 1099 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.50 % Allowed : 22.87 % Favored : 73.63 % 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: -0.51 (0.27), residues: 987 helix: 1.41 (0.28), residues: 340 sheet: -1.97 (0.33), residues: 212 loop : -0.79 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.001 PHE R 601 TYR 0.014 0.001 TYR R 785 ARG 0.014 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6203 (tp30) cc_final: 0.5981 (tt0) REVERT: B 171 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6130 (mp) REVERT: B 262 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4405 (ppp) REVERT: B 325 MET cc_start: 0.5865 (mmp) cc_final: 0.4570 (mmp) REVERT: R 753 TYR cc_start: 0.8628 (m-80) cc_final: 0.8051 (m-80) outliers start: 30 outliers final: 18 residues processed: 177 average time/residue: 0.7040 time to fit residues: 138.5193 Evaluate side-chains 170 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.0000 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8137 Z= 0.211 Angle : 0.594 9.320 11013 Z= 0.303 Chirality : 0.042 0.132 1244 Planarity : 0.004 0.043 1394 Dihedral : 4.571 18.694 1099 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.92 % Allowed : 24.04 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 987 helix: 1.40 (0.28), residues: 340 sheet: -2.03 (0.32), residues: 217 loop : -0.74 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.008 0.002 HIS A 357 PHE 0.026 0.002 PHE R 601 TYR 0.010 0.001 TYR N 117 ARG 0.013 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6216 (mp) REVERT: B 262 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4338 (ppp) REVERT: B 325 MET cc_start: 0.5841 (mmp) cc_final: 0.4508 (mmp) REVERT: R 753 TYR cc_start: 0.8658 (m-80) cc_final: 0.8131 (m-80) REVERT: R 801 LEU cc_start: 0.8531 (mm) cc_final: 0.8135 (mt) outliers start: 25 outliers final: 19 residues processed: 169 average time/residue: 0.7715 time to fit residues: 142.7338 Evaluate side-chains 171 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 632 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 62 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.157143 restraints weight = 8847.378| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.01 r_work: 0.3674 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8137 Z= 0.243 Angle : 0.617 12.059 11013 Z= 0.313 Chirality : 0.042 0.175 1244 Planarity : 0.004 0.056 1394 Dihedral : 4.647 18.749 1099 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.38 % Allowed : 24.27 % Favored : 72.35 % 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: -0.55 (0.27), residues: 987 helix: 1.39 (0.28), residues: 341 sheet: -2.01 (0.33), residues: 213 loop : -0.82 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.010 0.002 HIS A 357 PHE 0.020 0.002 PHE R 601 TYR 0.018 0.001 TYR R 785 ARG 0.013 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.34 seconds wall clock time: 59 minutes 9.36 seconds (3549.36 seconds total)