Starting phenix.real_space_refine on Sat Dec 28 22:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxr_36710/12_2024/8jxr_36710.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 871 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 41 5.16 5 C 5550 2.51 5 N 1421 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8616 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 929 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2649 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1536 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.64 Number of scatterers: 8616 At special positions: 0 Unit cell: (135.96, 122.776, 98.056, 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 41 16.00 O 1604 8.00 N 1421 7.00 C 5550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 186 " distance=2.08 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 307 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 17 sheets defined 41.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 51 removed outlier: 3.769A pdb=" N PHE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.029A pdb=" N ARG A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.069A pdb=" N PHE A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 95 through 127 Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.779A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 removed outlier: 3.953A pdb=" N ILE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 203 through 236 Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.477A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.602A pdb=" N PHE A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.670A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 Proline residue: C 49 - end of helix Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.703A pdb=" N GLY C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 removed outlier: 3.626A pdb=" N LYS C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.571A pdb=" N TRP C 95 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 154 through 165 removed outlier: 4.153A pdb=" N THR C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Proline residue: C 160 - end of helix removed outlier: 4.475A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 336 through 352 Processing helix chain 'C' and resid 357 through 370 removed outlier: 3.507A pdb=" N MET C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 504 through 517 removed outlier: 4.076A pdb=" N ALA C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.124A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.626A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.875A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 5.829A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 64 removed outlier: 7.091A pdb=" N GLY C 261 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL C 111 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C 263 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA9, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.153A pdb=" N VAL C 486 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS C 493 " --> pdb=" O ASP H 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.893A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.562A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.562A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.800A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.800A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN L 96 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 102 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.431A pdb=" N LEU L 140 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER L 182 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN L 142 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU L 180 " --> pdb=" O ASN L 142 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1293 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: 2.72 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2696 1.34 - 1.47: 2283 1.47 - 1.60: 3783 1.60 - 1.73: 0 1.73 - 1.86: 62 Bond restraints: 8824 Sorted by residual: bond pdb=" C14 7LD A 401 " pdb=" C16 7LD A 401 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C11 7LD A 401 " pdb=" C9 7LD A 401 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C10 7LD A 401 " pdb=" C14 7LD A 401 " ideal model delta sigma weight residual 1.501 1.398 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C15 7LD A 401 " pdb=" C7 7LD A 401 " ideal model delta sigma weight residual 1.491 1.395 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C3 7LD A 401 " pdb=" C7 7LD A 401 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.11e+01 ... (remaining 8819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 11853 1.82 - 3.64: 117 3.64 - 5.46: 25 5.46 - 7.28: 6 7.28 - 9.10: 1 Bond angle restraints: 12002 Sorted by residual: angle pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" C LEU A 190 " ideal model delta sigma weight residual 109.40 115.95 -6.55 1.63e+00 3.76e-01 1.61e+01 angle pdb=" N ILE C 109 " pdb=" CA ILE C 109 " pdb=" C ILE C 109 " ideal model delta sigma weight residual 111.48 108.95 2.53 9.40e-01 1.13e+00 7.23e+00 angle pdb=" CA LEU A 39 " pdb=" CB LEU A 39 " pdb=" CG LEU A 39 " ideal model delta sigma weight residual 116.30 125.40 -9.10 3.50e+00 8.16e-02 6.76e+00 angle pdb=" CA CYS A 298 " pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " ideal model delta sigma weight residual 114.40 120.20 -5.80 2.30e+00 1.89e-01 6.37e+00 angle pdb=" C ILE A 24 " pdb=" CA ILE A 24 " pdb=" CB ILE A 24 " ideal model delta sigma weight residual 111.97 108.84 3.13 1.28e+00 6.10e-01 6.00e+00 ... (remaining 11997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.34: 5110 30.34 - 60.68: 107 60.68 - 91.02: 14 91.02 - 121.36: 0 121.36 - 151.70: 1 Dihedral angle restraints: 5232 sinusoidal: 2017 harmonic: 3215 Sorted by residual: dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 163.95 -70.95 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" C16 7LD A 401 " pdb=" C17 7LD A 401 " pdb=" N3 7LD A 401 " pdb=" C18 7LD A 401 " ideal model delta sinusoidal sigma weight residual 91.75 -116.55 -151.70 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 186 " pdb=" CB CYS A 186 " ideal model delta sinusoidal sigma weight residual -86.00 -55.29 -30.71 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 5229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1352 0.141 - 0.281: 5 0.281 - 0.422: 3 0.422 - 0.562: 0 0.562 - 0.703: 1 Chirality restraints: 1361 Sorted by residual: chirality pdb=" C1 GLC D 2 " pdb=" O4 GLC D 1 " pdb=" C2 GLC D 2 " pdb=" O5 GLC D 2 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.24e+03 chirality pdb=" C14 7LD A 401 " pdb=" C10 7LD A 401 " pdb=" C13 7LD A 401 " pdb=" C16 7LD A 401 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.34 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1358 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 185 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C ASN A 185 " 0.027 2.00e-02 2.50e+03 pdb=" O ASN A 185 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS A 186 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 7LD A 401 " -0.001 2.00e-02 2.50e+03 8.05e-03 1.78e+00 pdb=" C15 7LD A 401 " -0.014 2.00e-02 2.50e+03 pdb=" C2 7LD A 401 " -0.006 2.00e-02 2.50e+03 pdb=" C3 7LD A 401 " 0.004 2.00e-02 2.50e+03 pdb=" C4 7LD A 401 " 0.001 2.00e-02 2.50e+03 pdb=" C5 7LD A 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 7LD A 401 " -0.011 2.00e-02 2.50e+03 pdb=" C7 7LD A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C8 7LD A 401 " 0.002 2.00e-02 2.50e+03 pdb=" C9 7LD A 401 " 0.016 2.00e-02 2.50e+03 pdb=" N1 7LD A 401 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 205 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.66e-01 pdb=" N PRO A 206 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.013 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 64 2.60 - 3.17: 7429 3.17 - 3.75: 13161 3.75 - 4.32: 17937 4.32 - 4.90: 30837 Nonbonded interactions: 69428 Sorted by model distance: nonbonded pdb=" OE1 GLU C 154 " pdb=" O6 GLC D 2 " model vdw 2.023 3.040 nonbonded pdb=" O PHE A 62 " pdb=" OG SER A 65 " model vdw 2.119 3.040 nonbonded pdb=" O ALA A 101 " pdb=" OG SER A 155 " model vdw 2.178 3.040 nonbonded pdb=" ND2 ASN H 207 " pdb=" OD1 ASN H 209 " model vdw 2.183 3.120 nonbonded pdb=" N GLU C 45 " pdb=" OE1 GLU C 45 " model vdw 2.275 3.120 ... (remaining 69423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.580 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.004 0.122 8824 Z= 0.259 Angle : 0.497 9.103 12002 Z= 0.263 Chirality : 0.047 0.703 1361 Planarity : 0.002 0.023 1505 Dihedral : 12.642 151.705 3148 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % 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: -1.28 (0.24), residues: 1072 helix: -0.02 (0.25), residues: 397 sheet: -1.31 (0.28), residues: 250 loop : -1.17 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 130 HIS 0.002 0.000 HIS H 35 PHE 0.004 0.000 PHE A 102 TYR 0.005 0.000 TYR H 95 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 127 SER cc_start: 0.7715 (t) cc_final: 0.7330 (p) REVERT: A 132 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 160 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7897 (mm-40) REVERT: A 339 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7666 (ttpp) REVERT: L 42 TYR cc_start: 0.8533 (m-80) cc_final: 0.8108 (m-80) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2330 time to fit residues: 54.8011 Evaluate side-chains 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 61 ASN B 83 ASN B 115 GLN B 123 HIS C 219 ASN C 333 ASN H 84 ASN H 165 ASN H 207 ASN L 27 GLN L 48 GLN L 163 ASN L 165 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 8824 Z= 0.481 Angle : 0.705 8.835 12002 Z= 0.362 Chirality : 0.047 0.191 1361 Planarity : 0.005 0.035 1505 Dihedral : 7.073 157.768 1239 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.49 % Allowed : 11.98 % Favored : 84.53 % 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: -0.15 (0.25), residues: 1072 helix: 0.85 (0.25), residues: 398 sheet: -0.42 (0.31), residues: 257 loop : -0.68 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 341 HIS 0.009 0.002 HIS H 35 PHE 0.023 0.003 PHE A 316 TYR 0.022 0.003 TYR L 97 ARG 0.007 0.001 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.957 Fit side-chains REVERT: A 103 ASP cc_start: 0.8711 (t70) cc_final: 0.8496 (t0) REVERT: A 160 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7831 (mm-40) REVERT: A 278 MET cc_start: 0.7863 (tpt) cc_final: 0.7590 (tpt) REVERT: B 64 LYS cc_start: 0.8370 (tptt) cc_final: 0.8103 (tppt) REVERT: B 112 GLN cc_start: 0.8178 (mt0) cc_final: 0.7353 (pm20) REVERT: C 43 LYS cc_start: 0.7637 (mmmt) cc_final: 0.7395 (mtpt) REVERT: C 333 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7656 (t0) REVERT: H 57 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8587 (p) REVERT: H 93 MET cc_start: 0.7913 (tpp) cc_final: 0.7470 (tpp) outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 0.1884 time to fit residues: 35.3095 Evaluate side-chains 111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS L 1 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8824 Z= 0.174 Angle : 0.511 7.125 12002 Z= 0.259 Chirality : 0.040 0.140 1361 Planarity : 0.003 0.044 1505 Dihedral : 6.501 142.038 1239 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.96 % Allowed : 14.60 % Favored : 83.44 % 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: 0.46 (0.26), residues: 1072 helix: 1.57 (0.26), residues: 403 sheet: -0.34 (0.32), residues: 246 loop : -0.44 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 164 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.001 PHE L 121 TYR 0.019 0.001 TYR H 155 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.977 Fit side-chains REVERT: A 52 ARG cc_start: 0.7251 (tpt170) cc_final: 0.6683 (tpt-90) REVERT: A 160 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7860 (mm-40) REVERT: A 344 LEU cc_start: 0.7927 (tt) cc_final: 0.7683 (tp) REVERT: B 64 LYS cc_start: 0.8329 (tptt) cc_final: 0.8087 (tppt) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 0.2221 time to fit residues: 35.1865 Evaluate side-chains 105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.0070 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 ASN L 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8824 Z= 0.176 Angle : 0.501 7.080 12002 Z= 0.252 Chirality : 0.040 0.137 1361 Planarity : 0.004 0.045 1505 Dihedral : 6.218 131.759 1239 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.83 % Allowed : 15.25 % Favored : 81.92 % 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: 0.76 (0.26), residues: 1072 helix: 1.89 (0.26), residues: 404 sheet: -0.24 (0.32), residues: 246 loop : -0.31 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 164 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE L 121 TYR 0.015 0.001 TYR H 155 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.968 Fit side-chains REVERT: A 52 ARG cc_start: 0.7214 (tpt170) cc_final: 0.6704 (tpt-90) REVERT: A 160 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7861 (mm-40) REVERT: A 278 MET cc_start: 0.7915 (tpt) cc_final: 0.7473 (tpt) REVERT: A 344 LEU cc_start: 0.8009 (tt) cc_final: 0.7766 (tp) REVERT: B 33 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8808 (mt) REVERT: B 43 LYS cc_start: 0.7278 (mtpt) cc_final: 0.7073 (mtpp) REVERT: B 64 LYS cc_start: 0.8311 (tptt) cc_final: 0.8048 (tppt) REVERT: B 112 GLN cc_start: 0.7928 (mt0) cc_final: 0.7202 (pm20) REVERT: C 333 ASN cc_start: 0.8020 (t0) cc_final: 0.7651 (t0) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 0.2152 time to fit residues: 36.5619 Evaluate side-chains 115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.0020 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8824 Z= 0.179 Angle : 0.500 7.051 12002 Z= 0.252 Chirality : 0.040 0.135 1361 Planarity : 0.004 0.037 1505 Dihedral : 6.085 124.163 1239 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.38 % Allowed : 14.60 % Favored : 82.03 % 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: 0.90 (0.26), residues: 1072 helix: 2.07 (0.26), residues: 403 sheet: -0.22 (0.32), residues: 246 loop : -0.27 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE A 288 TYR 0.013 0.001 TYR L 97 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.020 Fit side-chains REVERT: A 52 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6687 (tpt-90) REVERT: A 160 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7906 (mm-40) REVERT: A 278 MET cc_start: 0.7857 (tpt) cc_final: 0.7444 (tpt) REVERT: B 43 LYS cc_start: 0.7240 (mtpt) cc_final: 0.7035 (mtpp) REVERT: B 64 LYS cc_start: 0.8294 (tptt) cc_final: 0.8031 (tppt) REVERT: B 112 GLN cc_start: 0.7973 (mt0) cc_final: 0.7229 (pm20) REVERT: L 3 MET cc_start: 0.7995 (mmt) cc_final: 0.7788 (mmt) outliers start: 31 outliers final: 22 residues processed: 130 average time/residue: 0.2536 time to fit residues: 46.1472 Evaluate side-chains 119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8824 Z= 0.305 Angle : 0.571 7.502 12002 Z= 0.290 Chirality : 0.042 0.143 1361 Planarity : 0.004 0.037 1505 Dihedral : 6.347 121.227 1239 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.27 % Allowed : 15.47 % Favored : 81.26 % 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: 0.81 (0.26), residues: 1072 helix: 1.92 (0.26), residues: 404 sheet: -0.09 (0.31), residues: 260 loop : -0.35 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.019 0.002 PHE A 288 TYR 0.017 0.002 TYR L 97 ARG 0.004 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.915 Fit side-chains REVERT: A 52 ARG cc_start: 0.7178 (tpt170) cc_final: 0.6676 (tpt-90) REVERT: A 160 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7860 (mm-40) REVERT: A 278 MET cc_start: 0.7914 (tpt) cc_final: 0.7519 (tpt) REVERT: B 43 LYS cc_start: 0.7113 (mtpt) cc_final: 0.6912 (mtpp) REVERT: B 64 LYS cc_start: 0.8320 (tptt) cc_final: 0.8063 (tppt) outliers start: 30 outliers final: 26 residues processed: 123 average time/residue: 0.2011 time to fit residues: 34.6860 Evaluate side-chains 122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.002 0.037 8824 Z= 0.155 Angle : 0.510 6.663 12002 Z= 0.253 Chirality : 0.040 0.130 1361 Planarity : 0.003 0.037 1505 Dihedral : 5.669 101.432 1239 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.51 % Allowed : 16.99 % Favored : 80.50 % 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: 1.07 (0.26), residues: 1072 helix: 2.27 (0.26), residues: 403 sheet: -0.08 (0.31), residues: 257 loop : -0.27 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE L 121 TYR 0.032 0.001 TYR H 155 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.002 Fit side-chains REVERT: A 52 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6607 (tpt-90) REVERT: A 160 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7820 (mm-40) REVERT: A 278 MET cc_start: 0.7824 (tpt) cc_final: 0.7509 (tpt) REVERT: B 43 LYS cc_start: 0.7028 (mtpt) cc_final: 0.6761 (mtpp) REVERT: B 64 LYS cc_start: 0.8279 (tptt) cc_final: 0.8016 (tppt) REVERT: L 121 PHE cc_start: 0.7833 (m-80) cc_final: 0.7627 (m-80) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.2269 time to fit residues: 39.5893 Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8824 Z= 0.161 Angle : 0.518 7.474 12002 Z= 0.256 Chirality : 0.040 0.134 1361 Planarity : 0.003 0.037 1505 Dihedral : 5.007 75.787 1239 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 17.43 % Favored : 80.39 % 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: 1.22 (0.26), residues: 1072 helix: 2.36 (0.26), residues: 404 sheet: 0.02 (0.31), residues: 257 loop : -0.17 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE A 288 TYR 0.028 0.001 TYR H 155 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.896 Fit side-chains REVERT: A 52 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6626 (tpt-90) REVERT: A 160 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7853 (mm-40) REVERT: A 278 MET cc_start: 0.7839 (tpt) cc_final: 0.7521 (tpt) REVERT: B 43 LYS cc_start: 0.7011 (mtpt) cc_final: 0.6778 (mtpp) REVERT: B 64 LYS cc_start: 0.8288 (tptt) cc_final: 0.8028 (tppt) REVERT: B 88 GLU cc_start: 0.7777 (pt0) cc_final: 0.7510 (pm20) outliers start: 20 outliers final: 19 residues processed: 115 average time/residue: 0.2084 time to fit residues: 33.6075 Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8824 Z= 0.183 Angle : 0.526 7.506 12002 Z= 0.260 Chirality : 0.040 0.134 1361 Planarity : 0.003 0.037 1505 Dihedral : 4.476 42.351 1239 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.18 % Allowed : 17.43 % Favored : 80.39 % 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: 1.24 (0.26), residues: 1072 helix: 2.34 (0.26), residues: 405 sheet: 0.06 (0.31), residues: 255 loop : -0.14 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.019 0.001 PHE L 121 TYR 0.026 0.001 TYR H 155 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.895 Fit side-chains REVERT: A 52 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6613 (tpt-90) REVERT: A 160 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7825 (mm-40) REVERT: A 278 MET cc_start: 0.7837 (tpt) cc_final: 0.7542 (tpt) REVERT: B 43 LYS cc_start: 0.6925 (mtpt) cc_final: 0.6679 (mtpp) REVERT: B 64 LYS cc_start: 0.8290 (tptt) cc_final: 0.8020 (tppt) REVERT: C 91 TYR cc_start: 0.4834 (m-80) cc_final: 0.4558 (m-10) REVERT: C 349 ILE cc_start: 0.8700 (mm) cc_final: 0.8328 (mt) outliers start: 20 outliers final: 19 residues processed: 117 average time/residue: 0.2248 time to fit residues: 36.9860 Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8824 Z= 0.182 Angle : 0.540 11.177 12002 Z= 0.266 Chirality : 0.040 0.140 1361 Planarity : 0.003 0.037 1505 Dihedral : 4.322 40.448 1239 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.29 % Allowed : 17.32 % Favored : 80.39 % 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: 1.24 (0.26), residues: 1072 helix: 2.34 (0.26), residues: 407 sheet: 0.04 (0.31), residues: 258 loop : -0.14 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.001 PHE L 121 TYR 0.025 0.001 TYR H 155 ARG 0.004 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.040 Fit side-chains REVERT: A 52 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6600 (tpt-90) REVERT: A 160 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7854 (mm-40) REVERT: A 278 MET cc_start: 0.7834 (tpt) cc_final: 0.7539 (tpt) REVERT: B 34 MET cc_start: 0.8620 (mtp) cc_final: 0.8401 (ttm) REVERT: B 43 LYS cc_start: 0.6908 (mtpt) cc_final: 0.6665 (mtpp) REVERT: B 64 LYS cc_start: 0.8286 (tptt) cc_final: 0.8027 (tppt) REVERT: C 91 TYR cc_start: 0.4823 (m-80) cc_final: 0.4562 (m-10) REVERT: C 349 ILE cc_start: 0.8730 (mm) cc_final: 0.8374 (mt) outliers start: 21 outliers final: 20 residues processed: 114 average time/residue: 0.2058 time to fit residues: 33.6822 Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.166001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.138763 restraints weight = 9841.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136858 restraints weight = 17800.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136874 restraints weight = 16503.864| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8824 Z= 0.159 Angle : 0.524 10.138 12002 Z= 0.258 Chirality : 0.040 0.135 1361 Planarity : 0.003 0.037 1505 Dihedral : 4.242 45.888 1239 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.07 % Allowed : 17.43 % Favored : 80.50 % 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: 1.30 (0.26), residues: 1072 helix: 2.39 (0.25), residues: 406 sheet: 0.10 (0.31), residues: 258 loop : -0.11 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE L 121 TYR 0.025 0.001 TYR H 155 ARG 0.007 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.94 seconds wall clock time: 36 minutes 41.16 seconds (2201.16 seconds total)