Starting phenix.real_space_refine on Wed Mar 4 13:01:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6v_26381/03_2026/7u6v_26381.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5073 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 23 5.16 5 C 3168 2.51 5 N 854 2.21 5 O 1051 1.98 5 H 4901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9997 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4485 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4386 Chain: "B" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1058 Chain: "C" Number of atoms: 1105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1035 Chain: "D" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1054 Classifications: {'peptide': 69} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 1079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1064 Chain: "F" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1068 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1061 Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 99 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER A 99 " occ=0.62 residue: pdb=" N AARG A 119 " occ=0.59 ... (46 atoms not shown) pdb="HH22BARG A 119 " occ=0.41 residue: pdb=" N ASER A 278 " occ=0.27 ... (20 atoms not shown) pdb=" HG BSER A 278 " occ=0.73 residue: pdb=" N AVAL B 65 " occ=0.74 ... (30 atoms not shown) pdb="HG23BVAL B 65 " occ=0.26 residue: pdb=" N AGLU C 9 " occ=0.47 ... (28 atoms not shown) pdb=" HG3BGLU C 9 " occ=0.53 residue: pdb=" N ASER C 60 " occ=0.61 ... (20 atoms not shown) pdb=" HG BSER C 60 " occ=0.39 residue: pdb=" N ASER E 60 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER E 60 " occ=0.62 residue: pdb=" N ACYS F 3 " occ=0.68 ... (19 atoms not shown) pdb=" HG BCYS F 3 " occ=0.32 Time building chain proxies: 3.18, per 1000 atoms: 0.32 Number of scatterers: 9997 At special positions: 0 Unit cell: (78.356, 97.3264, 109.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 O 1051 8.00 N 854 7.00 C 3168 6.00 H 4901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 56 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 3 " - pdb=" SG CYS F 56 " distance=2.04 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 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 477.8 milliseconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 28.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 151 through 164 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.366A pdb=" N GLN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.042A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.079A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.600A pdb=" N TYR A 293 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.940A pdb=" N LEU B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 45 removed outlier: 4.522A pdb=" N LEU C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.695A pdb=" N LEU D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 45 Processing helix chain 'F' and resid 34 through 46 removed outlier: 4.578A pdb=" N LEU F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN F 40 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.105A pdb=" N LEU A 67 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 72 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 78 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.570A pdb=" N TYR A 189 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.849A pdb=" N GLY A 217 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU A 277 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG A 219 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 6 removed outlier: 6.485A pdb=" N ILE B 51 " --> pdb=" O CYS B 3 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 49 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.944A pdb=" N PHE C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU C 64 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.667A pdb=" N GLU D 64 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.742A pdb=" N THR D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.614A pdb=" N PHE E 10 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 23 " --> pdb=" O LYS E 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.213A pdb=" N ALA F 4 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.439A pdb=" N PHE F 10 " --> pdb=" O LYS F 22 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 575 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: 2.18 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4900 1.03 - 1.23: 25 1.23 - 1.43: 2212 1.43 - 1.62: 2904 1.62 - 1.82: 33 Bond restraints: 10074 Sorted by residual: bond pdb=" C SER A 37 " pdb=" N VAL A 38 " ideal model delta sigma weight residual 1.335 1.325 0.010 1.41e-02 5.03e+03 5.00e-01 bond pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.28e-02 6.10e+03 4.60e-01 bond pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.04e-02 9.25e+03 3.69e-01 bond pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " ideal model delta sigma weight residual 1.538 1.544 -0.007 1.10e-02 8.26e+03 3.50e-01 bond pdb=" CA GLU C 64 " pdb=" C GLU C 64 " ideal model delta sigma weight residual 1.529 1.523 0.006 1.04e-02 9.25e+03 3.43e-01 ... (remaining 10069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 17557 1.29 - 2.59: 499 2.59 - 3.88: 23 3.88 - 5.17: 3 5.17 - 6.47: 2 Bond angle restraints: 18084 Sorted by residual: angle pdb=" CB ARG A 156 " pdb=" CG ARG A 156 " pdb=" CD ARG A 156 " ideal model delta sigma weight residual 111.30 117.77 -6.47 2.30e+00 1.89e-01 7.91e+00 angle pdb=" CB ARG A 21 " pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " ideal model delta sigma weight residual 111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00 angle pdb=" N VAL C 21 " pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 110.05 107.66 2.39 1.09e+00 8.42e-01 4.79e+00 angle pdb=" N VAL A 38 " pdb=" CA VAL A 38 " pdb=" C VAL A 38 " ideal model delta sigma weight residual 110.21 107.80 2.41 1.13e+00 7.83e-01 4.56e+00 angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta sigma weight residual 110.12 113.12 -3.00 1.47e+00 4.63e-01 4.15e+00 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4365 17.97 - 35.94: 329 35.94 - 53.91: 73 53.91 - 71.88: 20 71.88 - 89.85: 5 Dihedral angle restraints: 4792 sinusoidal: 2567 harmonic: 2225 Sorted by residual: dihedral pdb=" CB CYS E 3 " pdb=" SG CYS E 3 " pdb=" SG CYS E 56 " pdb=" CB CYS E 56 " ideal model delta sinusoidal sigma weight residual -86.00 -56.34 -29.66 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 56 " pdb=" CB CYS C 56 " ideal model delta sinusoidal sigma weight residual -86.00 -57.64 -28.36 1 1.00e+01 1.00e-02 1.15e+01 dihedral pdb=" CA CYS D 3 " pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS D 56 " ideal model delta sinusoidal sigma weight residual 79.00 22.66 56.34 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 482 0.028 - 0.056: 202 0.056 - 0.085: 41 0.085 - 0.113: 48 0.113 - 0.141: 14 Chirality restraints: 787 Sorted by residual: chirality pdb=" CA VAL C 65 " pdb=" N VAL C 65 " pdb=" C VAL C 65 " pdb=" CB VAL C 65 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 784 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 210 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.010 9.50e-02 1.11e+02 6.87e-03 8.19e-01 pdb=" NE ARG A 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 36 " -0.005 2.00e-02 2.50e+03 8.94e-03 7.99e-01 pdb=" C GLN E 36 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN E 36 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO E 37 " -0.005 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 562 2.15 - 2.76: 20224 2.76 - 3.37: 29497 3.37 - 3.99: 37774 3.99 - 4.60: 57473 Nonbonded interactions: 145530 Sorted by model distance: nonbonded pdb=" OE2 GLU A 72 " pdb=" H TYR A 77 " model vdw 1.531 2.450 nonbonded pdb=" H HIS A 66 " pdb=" OH TYR A 139 " model vdw 1.550 2.450 nonbonded pdb=" OD1 ASP E 16 " pdb=" HG1 THR E 18 " model vdw 1.572 2.450 nonbonded pdb=" O ILE A 54 " pdb="HH11 ARG A 55 " model vdw 1.584 2.450 nonbonded pdb=" OD1 ASN C 14 " pdb=" H GLU C 15 " model vdw 1.591 2.450 ... (remaining 145525 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'C' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'D' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 59 or resid 62 t \ hrough 64 or resid 67 through 70)) selection = (chain 'E' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) selection = (chain 'F' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) } 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=0.12 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.060 Extract box with map and model: 0.090 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 12.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5179 Z= 0.124 Angle : 0.525 6.467 7024 Z= 0.315 Chirality : 0.041 0.141 787 Planarity : 0.002 0.037 908 Dihedral : 13.786 88.086 1861 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.57 % Allowed : 0.52 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.34), residues: 643 helix: 1.06 (0.47), residues: 159 sheet: -0.12 (0.42), residues: 150 loop : -0.62 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 156 TYR 0.013 0.001 TYR A 139 PHE 0.009 0.001 PHE A 81 TRP 0.007 0.001 TRP C 33 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5173) covalent geometry : angle 0.52429 ( 7012) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.78644 ( 12) hydrogen bonds : bond 0.18667 ( 214) hydrogen bonds : angle 6.85698 ( 575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.0664 (tpp) cc_final: 0.0398 (tpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1417 time to fit residues: 18.5654 Evaluate side-chains 83 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.094628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.060297 restraints weight = 203652.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.067818 restraints weight = 88666.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.073827 restraints weight = 51314.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.078612 restraints weight = 33128.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082346 restraints weight = 22763.364| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5179 Z= 0.160 Angle : 0.545 4.901 7024 Z= 0.305 Chirality : 0.042 0.134 787 Planarity : 0.005 0.039 908 Dihedral : 4.548 57.190 695 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.75 % Allowed : 3.85 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.33), residues: 643 helix: 0.64 (0.44), residues: 168 sheet: -0.39 (0.42), residues: 144 loop : -0.90 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 156 TYR 0.011 0.002 TYR A 293 PHE 0.013 0.002 PHE E 19 TRP 0.008 0.001 TRP B 33 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5173) covalent geometry : angle 0.54305 ( 7012) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.19937 ( 12) hydrogen bonds : bond 0.04475 ( 214) hydrogen bonds : angle 6.05972 ( 575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 LYS cc_start: 0.7730 (tptt) cc_final: 0.7480 (tptt) REVERT: F 47 MET cc_start: 0.6357 (mmm) cc_final: 0.6054 (mmt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1430 time to fit residues: 20.7859 Evaluate side-chains 94 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.094060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.059880 restraints weight = 205774.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067408 restraints weight = 88551.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.073438 restraints weight = 51013.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.078269 restraints weight = 32768.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.081916 restraints weight = 22355.795| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5179 Z= 0.157 Angle : 0.534 4.503 7024 Z= 0.299 Chirality : 0.042 0.135 787 Planarity : 0.004 0.061 908 Dihedral : 4.662 57.750 695 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.75 % Allowed : 3.15 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.31), residues: 643 helix: 0.17 (0.43), residues: 164 sheet: -0.39 (0.44), residues: 131 loop : -1.12 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.013 0.002 TYR B 13 PHE 0.020 0.002 PHE E 62 TRP 0.010 0.001 TRP E 29 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5173) covalent geometry : angle 0.53200 ( 7012) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.12826 ( 12) hydrogen bonds : bond 0.04335 ( 214) hydrogen bonds : angle 6.04840 ( 575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8343 (m-10) cc_final: 0.8083 (m-10) REVERT: F 47 MET cc_start: 0.6471 (mmm) cc_final: 0.6126 (mmt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1497 time to fit residues: 20.9323 Evaluate side-chains 90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.096430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.062795 restraints weight = 215430.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.070664 restraints weight = 92160.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076917 restraints weight = 52422.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.081628 restraints weight = 33273.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.085199 restraints weight = 22409.206| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 89 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5179 Z= 0.109 Angle : 0.512 5.152 7024 Z= 0.283 Chirality : 0.042 0.155 787 Planarity : 0.004 0.038 908 Dihedral : 4.564 60.450 695 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.57 % Allowed : 2.62 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.32), residues: 643 helix: 0.23 (0.43), residues: 168 sheet: -0.35 (0.45), residues: 129 loop : -0.99 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 156 TYR 0.010 0.001 TYR C 28 PHE 0.015 0.001 PHE E 62 TRP 0.008 0.001 TRP D 29 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5173) covalent geometry : angle 0.51047 ( 7012) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.06487 ( 12) hydrogen bonds : bond 0.03834 ( 214) hydrogen bonds : angle 5.79269 ( 575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 MET cc_start: 0.6380 (mmm) cc_final: 0.6000 (mmt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1439 time to fit residues: 22.3288 Evaluate side-chains 95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.095346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.064166 restraints weight = 168109.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.071402 restraints weight = 79998.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.077208 restraints weight = 46962.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.081541 restraints weight = 30339.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.084828 restraints weight = 20785.876| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 89 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5179 Z= 0.124 Angle : 0.511 4.435 7024 Z= 0.286 Chirality : 0.042 0.145 787 Planarity : 0.003 0.033 908 Dihedral : 4.567 60.017 695 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.57 % Allowed : 0.87 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.32), residues: 643 helix: 0.08 (0.42), residues: 168 sheet: -0.48 (0.44), residues: 136 loop : -0.95 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 156 TYR 0.011 0.001 TYR A 13 PHE 0.015 0.001 PHE E 62 TRP 0.011 0.001 TRP E 29 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5173) covalent geometry : angle 0.50986 ( 7012) SS BOND : bond 0.00287 ( 6) SS BOND : angle 1.05386 ( 12) hydrogen bonds : bond 0.03828 ( 214) hydrogen bonds : angle 5.84206 ( 575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9009 (t0) cc_final: 0.8657 (t70) REVERT: A 272 ASN cc_start: 0.8175 (m-40) cc_final: 0.7963 (m-40) REVERT: E 57 GLU cc_start: 0.8297 (mp0) cc_final: 0.8072 (mp0) REVERT: F 47 MET cc_start: 0.6474 (mmm) cc_final: 0.6097 (mmt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1465 time to fit residues: 21.0190 Evaluate side-chains 92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** F 43 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.092142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059357 restraints weight = 197951.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.066602 restraints weight = 90395.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.072272 restraints weight = 52958.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.076782 restraints weight = 34509.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.080257 restraints weight = 23854.610| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5179 Z= 0.171 Angle : 0.561 7.781 7024 Z= 0.316 Chirality : 0.042 0.151 787 Planarity : 0.004 0.039 908 Dihedral : 4.793 57.745 695 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.57 % Allowed : 2.80 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.31), residues: 643 helix: -0.03 (0.42), residues: 168 sheet: -0.58 (0.44), residues: 127 loop : -1.26 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 156 TYR 0.022 0.002 TYR A 139 PHE 0.019 0.002 PHE E 62 TRP 0.012 0.002 TRP E 29 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5173) covalent geometry : angle 0.55947 ( 7012) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.17534 ( 12) hydrogen bonds : bond 0.03896 ( 214) hydrogen bonds : angle 6.02659 ( 575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8344 (m-10) cc_final: 0.8076 (m-10) REVERT: A 272 ASN cc_start: 0.8226 (m-40) cc_final: 0.7988 (m110) REVERT: E 57 GLU cc_start: 0.8344 (mp0) cc_final: 0.8130 (mp0) REVERT: F 47 MET cc_start: 0.6515 (mmm) cc_final: 0.6041 (mmt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1406 time to fit residues: 19.5354 Evaluate side-chains 89 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN ** F 43 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.094265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.060476 restraints weight = 204048.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.068193 restraints weight = 87753.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.074239 restraints weight = 50039.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.078940 restraints weight = 31954.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.082490 restraints weight = 21695.831| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5179 Z= 0.123 Angle : 0.525 5.723 7024 Z= 0.293 Chirality : 0.042 0.139 787 Planarity : 0.004 0.053 908 Dihedral : 4.738 58.858 695 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.57 % Allowed : 1.92 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.31), residues: 643 helix: 0.02 (0.42), residues: 168 sheet: -0.58 (0.45), residues: 129 loop : -1.17 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.015 0.002 TYR A 293 PHE 0.015 0.002 PHE E 62 TRP 0.011 0.001 TRP E 29 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5173) covalent geometry : angle 0.52319 ( 7012) SS BOND : bond 0.00291 ( 6) SS BOND : angle 1.09574 ( 12) hydrogen bonds : bond 0.03691 ( 214) hydrogen bonds : angle 5.86974 ( 575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9076 (t0) cc_final: 0.8785 (t70) REVERT: A 272 ASN cc_start: 0.8248 (m-40) cc_final: 0.7999 (m110) REVERT: E 57 GLU cc_start: 0.8317 (mp0) cc_final: 0.8095 (mp0) REVERT: F 47 MET cc_start: 0.6548 (mmm) cc_final: 0.6064 (mmt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1303 time to fit residues: 18.6764 Evaluate side-chains 92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.095473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061866 restraints weight = 206507.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.069649 restraints weight = 87366.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075577 restraints weight = 49686.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.080288 restraints weight = 31846.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.083810 restraints weight = 21642.758| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 112 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5179 Z= 0.111 Angle : 0.521 6.053 7024 Z= 0.288 Chirality : 0.042 0.141 787 Planarity : 0.003 0.032 908 Dihedral : 4.691 59.637 695 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.57 % Allowed : 1.22 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.32), residues: 643 helix: 0.23 (0.43), residues: 163 sheet: -0.47 (0.45), residues: 129 loop : -1.10 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 21 TYR 0.011 0.001 TYR C 28 PHE 0.032 0.002 PHE C 19 TRP 0.016 0.001 TRP E 29 HIS 0.007 0.002 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5173) covalent geometry : angle 0.51955 ( 7012) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.05893 ( 12) hydrogen bonds : bond 0.03546 ( 214) hydrogen bonds : angle 5.75353 ( 575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8991 (t0) cc_final: 0.8665 (t70) REVERT: A 272 ASN cc_start: 0.8096 (m-40) cc_final: 0.7787 (m110) REVERT: E 57 GLU cc_start: 0.8250 (mp0) cc_final: 0.8007 (mp0) REVERT: F 47 MET cc_start: 0.6579 (mmm) cc_final: 0.6126 (mmt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1265 time to fit residues: 19.7407 Evaluate side-chains 95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.095566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.060700 restraints weight = 214137.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.068762 restraints weight = 88233.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074939 restraints weight = 49473.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.079700 restraints weight = 31469.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.083298 restraints weight = 21348.730| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 112 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5179 Z= 0.108 Angle : 0.519 5.888 7024 Z= 0.287 Chirality : 0.042 0.141 787 Planarity : 0.003 0.030 908 Dihedral : 4.663 60.189 695 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.57 % Allowed : 1.22 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.32), residues: 643 helix: 0.31 (0.43), residues: 163 sheet: -0.34 (0.45), residues: 129 loop : -1.07 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 21 TYR 0.010 0.001 TYR C 28 PHE 0.022 0.001 PHE C 19 TRP 0.017 0.001 TRP E 29 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5173) covalent geometry : angle 0.51763 ( 7012) SS BOND : bond 0.00268 ( 6) SS BOND : angle 1.03420 ( 12) hydrogen bonds : bond 0.03464 ( 214) hydrogen bonds : angle 5.65584 ( 575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASN cc_start: 0.7739 (m-40) cc_final: 0.7409 (m-40) REVERT: E 57 GLU cc_start: 0.8269 (mp0) cc_final: 0.8035 (mp0) REVERT: F 47 MET cc_start: 0.6486 (mmm) cc_final: 0.5964 (mmt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1313 time to fit residues: 19.3739 Evaluate side-chains 93 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.094159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.060568 restraints weight = 191048.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.068154 restraints weight = 83612.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.073958 restraints weight = 47963.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.078542 restraints weight = 30911.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082104 restraints weight = 21161.356| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5179 Z= 0.121 Angle : 0.530 8.708 7024 Z= 0.295 Chirality : 0.042 0.141 787 Planarity : 0.003 0.041 908 Dihedral : 4.697 59.656 695 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.57 % Allowed : 1.05 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.32), residues: 643 helix: 0.27 (0.43), residues: 168 sheet: -0.57 (0.46), residues: 126 loop : -0.96 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 156 TYR 0.012 0.001 TYR C 28 PHE 0.018 0.002 PHE C 19 TRP 0.021 0.002 TRP A 276 HIS 0.006 0.002 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 5173) covalent geometry : angle 0.52882 ( 7012) SS BOND : bond 0.00272 ( 6) SS BOND : angle 1.02011 ( 12) hydrogen bonds : bond 0.03431 ( 214) hydrogen bonds : angle 5.65785 ( 575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.4614 (tpp) cc_final: 0.3951 (tpp) REVERT: A 272 ASN cc_start: 0.7742 (m-40) cc_final: 0.7427 (m-40) REVERT: E 57 GLU cc_start: 0.8292 (mp0) cc_final: 0.8073 (mp0) REVERT: F 47 MET cc_start: 0.6499 (mmm) cc_final: 0.5983 (mmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1284 time to fit residues: 19.0325 Evaluate side-chains 91 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.094514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059947 restraints weight = 179036.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.067606 restraints weight = 79956.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.073413 restraints weight = 46115.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.078153 restraints weight = 29942.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.081764 restraints weight = 20620.675| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5179 Z= 0.116 Angle : 0.527 7.458 7024 Z= 0.293 Chirality : 0.042 0.139 787 Planarity : 0.003 0.039 908 Dihedral : 4.680 60.033 695 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.57 % Allowed : 1.22 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.32), residues: 643 helix: 0.13 (0.42), residues: 168 sheet: -0.56 (0.46), residues: 126 loop : -0.95 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 156 TYR 0.024 0.002 TYR A 139 PHE 0.017 0.001 PHE C 19 TRP 0.021 0.002 TRP A 276 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5173) covalent geometry : angle 0.52539 ( 7012) SS BOND : bond 0.00277 ( 6) SS BOND : angle 1.03617 ( 12) hydrogen bonds : bond 0.03385 ( 214) hydrogen bonds : angle 5.65124 ( 575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.60 seconds wall clock time: 51 minutes 21.18 seconds (3081.18 seconds total)