Starting phenix.real_space_refine on Tue Apr 29 19:20:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5b_29738/04_2025/8g5b_29738.cif" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5682 2.51 5 N 1503 2.21 5 O 1783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9009 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2100 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 252} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1012 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 775 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N VAL A 78 " occ=0.43 ... (5 atoms not shown) pdb=" CG2 VAL A 78 " occ=0.43 residue: pdb=" N ARG A 207 " occ=0.48 ... (9 atoms not shown) pdb=" NH2 ARG A 207 " occ=0.48 residue: pdb=" N SER A 227 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 227 " occ=0.54 residue: pdb=" N SER A 228 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 228 " occ=0.54 residue: pdb=" N TRP A 234 " occ=0.52 ... (12 atoms not shown) pdb=" CH2 TRP A 234 " occ=0.52 residue: pdb=" N MET A 260 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 260 " occ=0.50 residue: pdb=" N ILE A 274 " occ=0.62 ... (6 atoms not shown) pdb=" CD1 ILE A 274 " occ=0.62 residue: pdb=" N ASP A 275 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 275 " occ=0.62 Time building chain proxies: 5.48, per 1000 atoms: 0.61 Number of scatterers: 9009 At special positions: 0 Unit cell: (94.875, 123.75, 136.95, 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 1783 8.00 N 1503 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 NAG-ASN " NAG A 401 " - " ASN A 165 " " NAG A 402 " - " ASN A 285 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 32 sheets defined 9.7% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.735A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.711A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.983A pdb=" N THR I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 208 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.877A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.970A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 127 removed outlier: 3.636A pdb=" N SER M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.680A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.081A pdb=" N CYS A 277 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.785A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.722A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.109A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.287A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.287A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.280A pdb=" N ILE I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER I 57 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.845A pdb=" N TYR I 106 " --> pdb=" O ARG I 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.016A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.016A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 155 through 158 removed outlier: 3.923A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.209A pdb=" N TRP J 36 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR J 52 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP J 38 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR J 42 " --> pdb=" O GLY J 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.686A pdb=" N CYS J 97 " --> pdb=" O TRP J 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP J 120 " --> pdb=" O CYS J 97 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG J 99 " --> pdb=" O ASP J 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.429A pdb=" N ASN L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.429A pdb=" N ASN L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.841A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.004A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.661A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.323A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.828A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 993 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: 2.94 Time building geometry restraints manager: 2.85 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: 2842 1.34 - 1.46: 2359 1.46 - 1.59: 3964 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 9223 Sorted by residual: bond pdb=" N VAL L 13 " pdb=" CA VAL L 13 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" N ILE A 182 " pdb=" CA ILE A 182 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.52e+00 bond pdb=" N ILE M 21 " pdb=" CA ILE M 21 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.45e+00 bond pdb=" N THR L 5 " pdb=" CA THR L 5 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N GLU J 103 " pdb=" CA GLU J 103 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.39e+00 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12275 1.89 - 3.79: 232 3.79 - 5.68: 23 5.68 - 7.58: 1 7.58 - 9.47: 1 Bond angle restraints: 12532 Sorted by residual: angle pdb=" C GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta sigma weight residual 112.99 103.52 9.47 2.10e+00 2.27e-01 2.03e+01 angle pdb=" C ASP M 151 " pdb=" CA ASP M 151 " pdb=" CB ASP M 151 " ideal model delta sigma weight residual 115.79 111.19 4.60 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N PRO M 95 " pdb=" CA PRO M 95 " pdb=" CB PRO M 95 " ideal model delta sigma weight residual 103.25 107.09 -3.84 1.05e+00 9.07e-01 1.34e+01 angle pdb=" CA PRO M 95 " pdb=" N PRO M 95 " pdb=" CD PRO M 95 " ideal model delta sigma weight residual 112.00 107.29 4.71 1.40e+00 5.10e-01 1.13e+01 angle pdb=" CA GLU M 93 " pdb=" C GLU M 93 " pdb=" O GLU M 93 " ideal model delta sigma weight residual 121.98 118.40 3.58 1.13e+00 7.83e-01 1.00e+01 ... (remaining 12527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5063 17.66 - 35.33: 313 35.33 - 52.99: 89 52.99 - 70.65: 16 70.65 - 88.31: 16 Dihedral angle restraints: 5497 sinusoidal: 2139 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual 93.00 25.88 67.12 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 97 " pdb=" CB CYS J 97 " ideal model delta sinusoidal sigma weight residual 93.00 46.98 46.02 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS M 134 " pdb=" SG CYS M 134 " pdb=" SG CYS M 194 " pdb=" CB CYS M 194 " ideal model delta sinusoidal sigma weight residual 93.00 55.11 37.89 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 5494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1249 0.081 - 0.162: 135 0.162 - 0.243: 4 0.243 - 0.324: 0 0.324 - 0.405: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA GLU M 93 " pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CB GLU M 93 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA TYR M 94 " pdb=" N TYR M 94 " pdb=" C TYR M 94 " pdb=" CB TYR M 94 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1387 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR M 94 " -0.067 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO M 95 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO M 95 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO M 95 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 292 " 0.065 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO A 293 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN L 11 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO L 12 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO L 12 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 12 " -0.046 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1074 2.75 - 3.28: 8684 3.28 - 3.82: 14851 3.82 - 4.36: 18597 4.36 - 4.90: 32730 Nonbonded interactions: 75936 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 114 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OG SER A 228 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU M 195 " pdb=" OG1 THR M 206 " model vdw 2.243 3.040 nonbonded pdb=" O GLU M 187 " pdb=" NH2 ARG M 211 " model vdw 2.257 3.120 nonbonded pdb=" O PRO J 14 " pdb=" OG SER J 15 " model vdw 2.289 3.040 ... (remaining 75931 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=0.00 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.820 Find NCS groups from input model: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 0.042 9237 Z= 0.289 Angle : 0.630 9.473 12562 Z= 0.365 Chirality : 0.047 0.405 1390 Planarity : 0.005 0.098 1597 Dihedral : 13.651 88.313 3327 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.70 % Allowed : 0.80 % Favored : 98.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 12.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1157 helix: 0.62 (0.79), residues: 42 sheet: 0.43 (0.23), residues: 506 loop : 0.23 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.004 0.001 HIS M 91 PHE 0.017 0.001 PHE N 46 TYR 0.020 0.002 TYR J 35 ARG 0.005 0.001 ARG M 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.28851 ( 6) hydrogen bonds : bond 0.21289 ( 355) hydrogen bonds : angle 9.34750 ( 993) SS BOND : bond 0.00308 ( 12) SS BOND : angle 1.16081 ( 24) covalent geometry : bond 0.00589 ( 9223) covalent geometry : angle 0.62826 (12532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 1.058 Fit side-chains REVERT: A 110 SER cc_start: 0.8084 (t) cc_final: 0.7518 (m) REVERT: A 140 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7234 (mmtt) REVERT: H 23 LYS cc_start: 0.7968 (tptp) cc_final: 0.7725 (tptt) REVERT: H 34 MET cc_start: 0.8098 (mmm) cc_final: 0.7830 (tpp) REVERT: H 46 GLU cc_start: 0.8032 (tt0) cc_final: 0.7708 (tt0) REVERT: H 65 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7742 (ttmt) REVERT: I 3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7929 (pt0) REVERT: I 5 GLN cc_start: 0.7847 (tp40) cc_final: 0.7620 (tp40) REVERT: I 23 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7778 (tttm) REVERT: I 65 LYS cc_start: 0.8029 (tppt) cc_final: 0.7635 (tptp) REVERT: I 210 LYS cc_start: 0.7970 (tttp) cc_final: 0.7494 (ttpt) REVERT: I 213 LYS cc_start: 0.6977 (tptt) cc_final: 0.6695 (tptt) REVERT: J 25 SER cc_start: 0.7840 (m) cc_final: 0.7482 (p) REVERT: J 45 LYS cc_start: 0.8383 (mttp) cc_final: 0.7722 (mtpt) REVERT: J 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8156 (m-30) REVERT: L 27 LYS cc_start: 0.7577 (ttmt) cc_final: 0.6781 (tttm) REVERT: L 75 ASP cc_start: 0.6888 (p0) cc_final: 0.6419 (m-30) REVERT: M 77 SER cc_start: 0.8093 (p) cc_final: 0.7883 (t) REVERT: M 165 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6925 (mm-30) REVERT: M 183 LYS cc_start: 0.7558 (tttm) cc_final: 0.7349 (tttt) REVERT: N 65 SER cc_start: 0.8367 (t) cc_final: 0.8082 (m) REVERT: N 96 GLN cc_start: 0.8220 (mp10) cc_final: 0.7819 (mp10) outliers start: 7 outliers final: 2 residues processed: 198 average time/residue: 0.2380 time to fit residues: 63.4796 Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 189 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103063 restraints weight = 10515.688| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.19 r_work: 0.2734 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9237 Z= 0.212 Angle : 0.643 8.084 12562 Z= 0.338 Chirality : 0.047 0.206 1390 Planarity : 0.005 0.073 1597 Dihedral : 5.778 50.469 1308 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 7.49 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1157 helix: 0.80 (0.76), residues: 43 sheet: 0.47 (0.22), residues: 515 loop : 0.20 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.006 0.001 HIS H 35 PHE 0.016 0.002 PHE N 46 TYR 0.037 0.002 TYR J 35 ARG 0.003 0.001 ARG J 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 2) link_NAG-ASN : angle 1.30348 ( 6) hydrogen bonds : bond 0.03942 ( 355) hydrogen bonds : angle 6.51890 ( 993) SS BOND : bond 0.00525 ( 12) SS BOND : angle 1.49087 ( 24) covalent geometry : bond 0.00496 ( 9223) covalent geometry : angle 0.64018 (12532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 241 ASP cc_start: 0.8309 (t0) cc_final: 0.7881 (t70) REVERT: H 23 LYS cc_start: 0.8346 (tptp) cc_final: 0.8116 (tptt) REVERT: H 31 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7859 (mtt180) REVERT: H 34 MET cc_start: 0.8626 (mmm) cc_final: 0.8415 (tpp) REVERT: H 46 GLU cc_start: 0.8579 (tt0) cc_final: 0.8369 (tt0) REVERT: H 65 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8125 (tttt) REVERT: H 80 TYR cc_start: 0.8337 (m-80) cc_final: 0.7980 (m-80) REVERT: I 65 LYS cc_start: 0.8156 (tppt) cc_final: 0.7757 (tptp) REVERT: L 27 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7311 (tttm) REVERT: L 55 GLN cc_start: 0.7961 (mt0) cc_final: 0.7701 (mt0) REVERT: L 65 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6815 (m-30) REVERT: L 66 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6796 (mtm110) REVERT: L 87 ASP cc_start: 0.7726 (m-30) cc_final: 0.7526 (m-30) REVERT: M 77 SER cc_start: 0.8410 (p) cc_final: 0.8193 (t) REVERT: M 133 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7767 (t) REVERT: M 160 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6732 (mm-40) REVERT: M 165 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7203 (mm-30) REVERT: N 65 SER cc_start: 0.8508 (t) cc_final: 0.8187 (m) outliers start: 16 outliers final: 7 residues processed: 154 average time/residue: 0.2006 time to fit residues: 43.6452 Evaluate side-chains 146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098397 restraints weight = 10669.188| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2700 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9237 Z= 0.158 Angle : 0.566 6.668 12562 Z= 0.297 Chirality : 0.044 0.158 1390 Planarity : 0.004 0.063 1597 Dihedral : 5.059 49.809 1305 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.20 % Allowed : 10.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.50 (0.25), residues: 1157 helix: 1.06 (0.77), residues: 44 sheet: 0.57 (0.22), residues: 517 loop : 0.19 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE N 46 TYR 0.024 0.002 TYR J 35 ARG 0.003 0.000 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 2) link_NAG-ASN : angle 0.99510 ( 6) hydrogen bonds : bond 0.03447 ( 355) hydrogen bonds : angle 5.97371 ( 993) SS BOND : bond 0.00395 ( 12) SS BOND : angle 1.23697 ( 24) covalent geometry : bond 0.00363 ( 9223) covalent geometry : angle 0.56410 (12532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.8125 (mmp) cc_final: 0.7697 (mmt) REVERT: H 23 LYS cc_start: 0.8331 (tptp) cc_final: 0.8052 (tptt) REVERT: H 31 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7814 (mtt180) REVERT: H 34 MET cc_start: 0.8734 (mmm) cc_final: 0.8525 (tpp) REVERT: H 80 TYR cc_start: 0.8277 (m-80) cc_final: 0.7929 (m-80) REVERT: I 3 GLN cc_start: 0.8609 (pt0) cc_final: 0.8371 (pt0) REVERT: I 5 GLN cc_start: 0.8671 (tp40) cc_final: 0.8426 (tp40) REVERT: I 65 LYS cc_start: 0.8067 (tppt) cc_final: 0.7658 (tptp) REVERT: J 45 LYS cc_start: 0.8521 (mttp) cc_final: 0.7941 (mtpt) REVERT: L 27 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7289 (tttm) REVERT: L 55 GLN cc_start: 0.7986 (mt0) cc_final: 0.7680 (mt0) REVERT: L 65 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: L 66 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6805 (mtm110) REVERT: M 133 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7736 (t) REVERT: M 160 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6725 (mm-40) REVERT: M 195 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7100 (mm-30) REVERT: N 65 SER cc_start: 0.8514 (t) cc_final: 0.8211 (m) outliers start: 22 outliers final: 15 residues processed: 149 average time/residue: 0.2155 time to fit residues: 45.0154 Evaluate side-chains 149 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN L 50 GLN M 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097389 restraints weight = 10583.715| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.31 r_work: 0.2663 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9237 Z= 0.204 Angle : 0.598 7.328 12562 Z= 0.311 Chirality : 0.045 0.174 1390 Planarity : 0.005 0.057 1597 Dihedral : 5.138 50.366 1303 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.40 % Allowed : 11.29 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.41 (0.25), residues: 1157 helix: 0.87 (0.77), residues: 45 sheet: 0.55 (0.22), residues: 513 loop : 0.08 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.005 0.001 HIS M 91 PHE 0.011 0.002 PHE J 80 TYR 0.025 0.002 TYR J 35 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 2) link_NAG-ASN : angle 1.19749 ( 6) hydrogen bonds : bond 0.03456 ( 355) hydrogen bonds : angle 5.89503 ( 993) SS BOND : bond 0.00453 ( 12) SS BOND : angle 1.34945 ( 24) covalent geometry : bond 0.00476 ( 9223) covalent geometry : angle 0.59484 (12532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.8234 (mmp) cc_final: 0.7706 (mmt) REVERT: A 195 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: A 241 ASP cc_start: 0.8350 (t0) cc_final: 0.8077 (t0) REVERT: H 31 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7803 (mtt180) REVERT: I 65 LYS cc_start: 0.8108 (tppt) cc_final: 0.7636 (tptp) REVERT: L 27 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7358 (tttm) REVERT: L 55 GLN cc_start: 0.7996 (mt0) cc_final: 0.7757 (mt0) REVERT: L 65 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: M 133 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7679 (t) REVERT: M 160 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6819 (mm-40) REVERT: M 195 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7215 (mm-30) REVERT: N 65 SER cc_start: 0.8519 (t) cc_final: 0.8197 (m) outliers start: 34 outliers final: 26 residues processed: 154 average time/residue: 0.2197 time to fit residues: 47.0677 Evaluate side-chains 161 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 0.0020 chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN I 109 GLN L 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100747 restraints weight = 10529.149| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.39 r_work: 0.2747 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9237 Z= 0.117 Angle : 0.527 7.294 12562 Z= 0.275 Chirality : 0.043 0.167 1390 Planarity : 0.004 0.054 1597 Dihedral : 4.820 49.808 1303 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 12.49 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.57 (0.25), residues: 1157 helix: 1.23 (0.77), residues: 45 sheet: 0.66 (0.23), residues: 513 loop : 0.18 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.018 0.001 TYR J 35 ARG 0.002 0.000 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 0.82079 ( 6) hydrogen bonds : bond 0.02879 ( 355) hydrogen bonds : angle 5.48954 ( 993) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.11154 ( 24) covalent geometry : bond 0.00266 ( 9223) covalent geometry : angle 0.52464 (12532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.8055 (mmp) cc_final: 0.7577 (mmt) REVERT: H 80 TYR cc_start: 0.8248 (m-80) cc_final: 0.7823 (m-80) REVERT: H 109 VAL cc_start: 0.8897 (p) cc_final: 0.8666 (m) REVERT: I 3 GLN cc_start: 0.8564 (pt0) cc_final: 0.8326 (pt0) REVERT: I 65 LYS cc_start: 0.8024 (tppt) cc_final: 0.7591 (tptp) REVERT: J 45 LYS cc_start: 0.8521 (mttp) cc_final: 0.7947 (mtpt) REVERT: L 27 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7350 (tttm) REVERT: L 55 GLN cc_start: 0.7901 (mt0) cc_final: 0.7658 (mt0) REVERT: L 65 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: L 66 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6754 (mtm110) REVERT: M 160 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6842 (mm-40) REVERT: M 195 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7186 (mm-30) REVERT: N 65 SER cc_start: 0.8406 (t) cc_final: 0.8104 (m) outliers start: 28 outliers final: 17 residues processed: 160 average time/residue: 0.2415 time to fit residues: 54.1286 Evaluate side-chains 150 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN H 5 GLN I 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104135 restraints weight = 10475.907| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.33 r_work: 0.2687 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9237 Z= 0.249 Angle : 0.627 9.245 12562 Z= 0.325 Chirality : 0.046 0.174 1390 Planarity : 0.005 0.054 1597 Dihedral : 5.149 50.367 1303 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.50 % Allowed : 12.69 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.39 (0.25), residues: 1157 helix: 0.87 (0.75), residues: 45 sheet: 0.51 (0.22), residues: 515 loop : 0.10 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 101 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.002 PHE I 102 TYR 0.025 0.002 TYR J 35 ARG 0.003 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 1.28928 ( 6) hydrogen bonds : bond 0.03527 ( 355) hydrogen bonds : angle 5.76970 ( 993) SS BOND : bond 0.00503 ( 12) SS BOND : angle 1.88137 ( 24) covalent geometry : bond 0.00585 ( 9223) covalent geometry : angle 0.62166 (12532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.8229 (mmt) cc_final: 0.7674 (mmt) REVERT: A 195 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: H 109 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8647 (m) REVERT: I 5 GLN cc_start: 0.8559 (tp40) cc_final: 0.8301 (tp40) REVERT: I 65 LYS cc_start: 0.8108 (tppt) cc_final: 0.7609 (tptp) REVERT: I 109 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8372 (pt0) REVERT: J 108 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8366 (m) REVERT: L 23 CYS cc_start: 0.8379 (t) cc_final: 0.7819 (t) REVERT: L 27 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7333 (tttm) REVERT: L 65 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: L 66 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6621 (mtm110) REVERT: M 160 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6965 (mm-40) REVERT: M 195 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6913 (mm-30) REVERT: N 65 SER cc_start: 0.8537 (t) cc_final: 0.8208 (m) outliers start: 35 outliers final: 25 residues processed: 159 average time/residue: 0.2099 time to fit residues: 47.1632 Evaluate side-chains 159 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN I 109 GLN L 50 GLN L 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.103040 restraints weight = 10633.512| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.51 r_work: 0.2720 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9237 Z= 0.133 Angle : 0.549 8.306 12562 Z= 0.286 Chirality : 0.043 0.191 1390 Planarity : 0.004 0.053 1597 Dihedral : 4.934 49.987 1303 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.80 % Allowed : 13.69 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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 (0.25), residues: 1157 helix: 1.20 (0.76), residues: 45 sheet: 0.60 (0.22), residues: 513 loop : 0.15 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.017 0.001 TYR J 35 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 2) link_NAG-ASN : angle 0.89286 ( 6) hydrogen bonds : bond 0.02963 ( 355) hydrogen bonds : angle 5.46672 ( 993) SS BOND : bond 0.00332 ( 12) SS BOND : angle 1.42482 ( 24) covalent geometry : bond 0.00306 ( 9223) covalent geometry : angle 0.54588 (12532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7619 (mmtt) REVERT: A 168 MET cc_start: 0.8121 (mmt) cc_final: 0.7656 (mmt) REVERT: A 195 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: H 23 LYS cc_start: 0.8345 (tptp) cc_final: 0.8059 (tptt) REVERT: H 109 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8675 (m) REVERT: I 65 LYS cc_start: 0.8082 (tppt) cc_final: 0.7651 (tptp) REVERT: J 45 LYS cc_start: 0.8456 (mttp) cc_final: 0.7891 (mtpt) REVERT: J 108 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (m) REVERT: L 27 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7321 (tttm) REVERT: L 65 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: L 66 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6688 (mtm110) REVERT: M 160 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6927 (mm-40) REVERT: M 195 GLU cc_start: 0.7678 (mm-30) cc_final: 0.6962 (mm-30) REVERT: N 65 SER cc_start: 0.8421 (t) cc_final: 0.8118 (m) outliers start: 28 outliers final: 20 residues processed: 162 average time/residue: 0.2745 time to fit residues: 63.9661 Evaluate side-chains 157 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102057 restraints weight = 10715.381| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.83 r_work: 0.2690 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9237 Z= 0.167 Angle : 0.571 10.905 12562 Z= 0.295 Chirality : 0.044 0.201 1390 Planarity : 0.004 0.052 1597 Dihedral : 4.964 50.170 1303 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.40 % Allowed : 13.39 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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 (0.25), residues: 1157 helix: 1.20 (0.76), residues: 45 sheet: 0.58 (0.22), residues: 515 loop : 0.09 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS M 91 PHE 0.011 0.001 PHE J 80 TYR 0.020 0.002 TYR J 35 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.01084 ( 6) hydrogen bonds : bond 0.03091 ( 355) hydrogen bonds : angle 5.45991 ( 993) SS BOND : bond 0.00379 ( 12) SS BOND : angle 1.44310 ( 24) covalent geometry : bond 0.00391 ( 9223) covalent geometry : angle 0.56730 (12532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7671 (mmtt) REVERT: A 168 MET cc_start: 0.8195 (mmt) cc_final: 0.7737 (mmt) REVERT: A 195 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: H 23 LYS cc_start: 0.8296 (tptp) cc_final: 0.8015 (tptt) REVERT: H 109 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8659 (m) REVERT: I 63 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8411 (ttmt) REVERT: I 65 LYS cc_start: 0.8097 (tppt) cc_final: 0.7659 (tptp) REVERT: J 45 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7879 (mtpt) REVERT: J 108 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8350 (m) REVERT: L 27 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7325 (tttm) REVERT: L 65 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: L 66 ARG cc_start: 0.6886 (mtp180) cc_final: 0.6543 (mtm110) REVERT: M 160 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6956 (mm-40) REVERT: M 195 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6951 (mm-30) REVERT: N 65 SER cc_start: 0.8471 (t) cc_final: 0.8172 (m) outliers start: 34 outliers final: 27 residues processed: 164 average time/residue: 0.2300 time to fit residues: 51.4719 Evaluate side-chains 167 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102118 restraints weight = 10576.837| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.30 r_work: 0.2682 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9237 Z= 0.145 Angle : 0.550 10.468 12562 Z= 0.285 Chirality : 0.043 0.212 1390 Planarity : 0.004 0.052 1597 Dihedral : 4.891 50.149 1303 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.80 % Allowed : 12.99 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.48 (0.25), residues: 1157 helix: 1.25 (0.76), residues: 45 sheet: 0.58 (0.22), residues: 515 loop : 0.12 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.018 0.001 TYR J 35 ARG 0.007 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 0.87612 ( 6) hydrogen bonds : bond 0.02977 ( 355) hydrogen bonds : angle 5.35444 ( 993) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.35126 ( 24) covalent geometry : bond 0.00337 ( 9223) covalent geometry : angle 0.54733 (12532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7609 (mmtt) REVERT: A 195 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: H 23 LYS cc_start: 0.8304 (tptp) cc_final: 0.8032 (tptt) REVERT: H 109 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8642 (m) REVERT: I 63 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8350 (ttmt) REVERT: J 45 LYS cc_start: 0.8438 (mttp) cc_final: 0.7852 (mtpt) REVERT: J 75 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6109 (ttm) REVERT: J 108 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (m) REVERT: L 27 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7291 (tttm) REVERT: L 65 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: M 160 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6967 (mm-40) REVERT: M 195 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6936 (mm-30) REVERT: N 65 SER cc_start: 0.8448 (t) cc_final: 0.8151 (m) outliers start: 38 outliers final: 31 residues processed: 161 average time/residue: 0.2615 time to fit residues: 58.6028 Evaluate side-chains 166 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.141119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.104106 restraints weight = 10280.925| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.27 r_work: 0.2736 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9237 Z= 0.318 Angle : 0.679 10.597 12562 Z= 0.351 Chirality : 0.048 0.207 1390 Planarity : 0.005 0.053 1597 Dihedral : 5.368 50.480 1303 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.10 % Allowed : 12.89 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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 (0.24), residues: 1157 helix: 0.75 (0.76), residues: 45 sheet: 0.37 (0.22), residues: 522 loop : -0.09 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.009 0.002 HIS H 35 PHE 0.015 0.002 PHE I 64 TYR 0.028 0.002 TYR J 35 ARG 0.005 0.001 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 2) link_NAG-ASN : angle 1.54597 ( 6) hydrogen bonds : bond 0.03780 ( 355) hydrogen bonds : angle 5.84286 ( 993) SS BOND : bond 0.00558 ( 12) SS BOND : angle 1.74253 ( 24) covalent geometry : bond 0.00750 ( 9223) covalent geometry : angle 0.67468 (12532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7670 (mmtt) REVERT: A 195 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: H 109 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8586 (m) REVERT: J 75 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6388 (ttm) REVERT: L 23 CYS cc_start: 0.8395 (t) cc_final: 0.7845 (t) REVERT: L 27 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7236 (tttm) REVERT: L 65 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6448 (m-30) REVERT: M 160 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6998 (mm-40) REVERT: M 195 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6947 (mm-30) REVERT: N 65 SER cc_start: 0.8595 (t) cc_final: 0.8226 (m) outliers start: 41 outliers final: 32 residues processed: 161 average time/residue: 0.2163 time to fit residues: 48.5208 Evaluate side-chains 165 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103622 restraints weight = 10583.305| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.60 r_work: 0.2705 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9237 Z= 0.108 Angle : 0.544 10.105 12562 Z= 0.280 Chirality : 0.043 0.236 1390 Planarity : 0.004 0.051 1597 Dihedral : 4.845 48.991 1303 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.50 % Allowed : 14.69 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.41 (0.25), residues: 1157 helix: 1.16 (0.76), residues: 45 sheet: 0.51 (0.22), residues: 528 loop : 0.10 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.002 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.013 0.001 TYR J 35 ARG 0.009 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 0.82287 ( 6) hydrogen bonds : bond 0.02841 ( 355) hydrogen bonds : angle 5.29612 ( 993) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.25158 ( 24) covalent geometry : bond 0.00245 ( 9223) covalent geometry : angle 0.54161 (12532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6861.97 seconds wall clock time: 119 minutes 34.07 seconds (7174.07 seconds total)