Starting phenix.real_space_refine on Thu Jul 2 22:06:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2026/7xqg_33395.cif" } resolution = 3.8 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 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 P 6 5.49 5 S 48 5.16 5 C 6846 2.51 5 N 1566 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.55, per 1000 atoms: 0.15 Number of scatterers: 10206 At special positions: 0 Unit cell: (106, 111.088, 99.216, 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 48 16.00 P 6 15.00 O 1740 8.00 N 1566 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 336.8 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 177 Processing helix chain 'A' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 177 Processing helix chain 'B' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 177 Processing helix chain 'C' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.602A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 177 Processing helix chain 'D' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.534A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.795A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 177 Processing helix chain 'E' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.511A pdb=" N GLN F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 177 Processing helix chain 'F' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2088 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: 1.37 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1597 1.33 - 1.45: 2897 1.45 - 1.57: 5910 1.57 - 1.69: 12 1.69 - 1.81: 60 Bond restraints: 10476 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.95e-01 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.90e-01 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.82e-01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 13864 1.22 - 2.44: 244 2.44 - 3.66: 52 3.66 - 4.88: 12 4.88 - 6.10: 18 Bond angle restraints: 14190 Sorted by residual: angle pdb=" C SER C 201 " pdb=" N ARG C 202 " pdb=" CA ARG C 202 " ideal model delta sigma weight residual 121.80 127.27 -5.47 2.44e+00 1.68e-01 5.02e+00 angle pdb=" C SER F 201 " pdb=" N ARG F 202 " pdb=" CA ARG F 202 " ideal model delta sigma weight residual 121.80 127.26 -5.46 2.44e+00 1.68e-01 5.01e+00 angle pdb=" C SER E 201 " pdb=" N ARG E 202 " pdb=" CA ARG E 202 " ideal model delta sigma weight residual 121.80 127.25 -5.45 2.44e+00 1.68e-01 4.99e+00 angle pdb=" C SER A 201 " pdb=" N ARG A 202 " pdb=" CA ARG A 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 angle pdb=" C SER D 201 " pdb=" N ARG D 202 " pdb=" CA ARG D 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 ... (remaining 14185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 5394 11.96 - 23.93: 480 23.93 - 35.89: 121 35.89 - 47.86: 53 47.86 - 59.82: 30 Dihedral angle restraints: 6078 sinusoidal: 2550 harmonic: 3528 Sorted by residual: dihedral pdb=" N PHE A 212 " pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sinusoidal sigma weight residual 180.00 -126.50 -53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE C 212 " pdb=" CA PHE C 212 " pdb=" CB PHE C 212 " pdb=" CG PHE C 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.52 -53.48 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE B 212 " pdb=" CA PHE B 212 " pdb=" CB PHE B 212 " pdb=" CG PHE B 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.53 -53.47 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 6075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 878 0.021 - 0.041: 409 0.041 - 0.062: 227 0.062 - 0.083: 53 0.083 - 0.103: 35 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.66e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 chirality pdb=" CA VAL C 184 " pdb=" N VAL C 184 " pdb=" C VAL C 184 " pdb=" CB VAL C 184 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 1599 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 190 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO E 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO E 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 191 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 190 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO C 191 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 190 " 0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO F 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.011 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2430 2.79 - 3.32: 10217 3.32 - 3.85: 16371 3.85 - 4.37: 16449 4.37 - 4.90: 30061 Nonbonded interactions: 75528 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG1 THR C 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU F 35 " pdb=" OG1 THR F 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU D 35 " pdb=" OG1 THR D 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG1 THR A 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.268 3.040 ... (remaining 75523 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 0.018 10494 Z= 0.099 Angle : 0.459 6.101 14226 Z= 0.234 Chirality : 0.032 0.103 1602 Planarity : 0.002 0.021 1674 Dihedral : 11.189 59.820 3744 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.52 % Favored : 97.97 % Rotamer: Outliers : 5.00 % Allowed : 3.89 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.98 (0.24), residues: 1182 helix: 2.75 (0.17), residues: 834 sheet: 3.07 (0.70), residues: 66 loop : -0.84 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 153 TYR 0.008 0.001 TYR C 155 PHE 0.006 0.001 PHE E 32 TRP 0.003 0.001 TRP A 78 HIS 0.001 0.000 HIS F 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (10476) covalent geometry : angle 0.45865 / 0.23 (14190) SS BOND : bond 0.00163 / 0.10 ( 18) SS BOND : angle 0.50849 / 0.36 ( 36) hydrogen bonds : bond 0.08910 / 5.66 ( 702) hydrogen bonds : angle 2.97157 / 2.18 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 0.472 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: A 47 ASP cc_start: 0.8362 (p0) cc_final: 0.8145 (p0) REVERT: A 173 GLN cc_start: 0.9564 (tt0) cc_final: 0.8945 (tm-30) REVERT: B 47 ASP cc_start: 0.8327 (p0) cc_final: 0.8048 (p0) REVERT: B 92 TYR cc_start: 0.9254 (t80) cc_final: 0.9052 (t80) REVERT: B 103 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9290 (mm-30) REVERT: B 173 GLN cc_start: 0.9582 (tt0) cc_final: 0.8986 (tm-30) REVERT: C 47 ASP cc_start: 0.8056 (p0) cc_final: 0.7755 (p0) REVERT: C 92 TYR cc_start: 0.9306 (t80) cc_final: 0.9097 (t80) REVERT: C 173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9013 (tm-30) REVERT: D 47 ASP cc_start: 0.8142 (p0) cc_final: 0.7876 (p0) REVERT: D 103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9096 (tp30) REVERT: E 47 ASP cc_start: 0.8197 (p0) cc_final: 0.7834 (p0) REVERT: E 101 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8595 (tpt170) REVERT: E 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.8999 (tm-30) REVERT: F 47 ASP cc_start: 0.8159 (p0) cc_final: 0.7888 (p0) REVERT: F 101 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8688 (tpt170) REVERT: F 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9033 (tm-30) REVERT: F 202 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8539 (ptp90) outliers start: 54 outliers final: 19 residues processed: 340 average time/residue: 0.1083 time to fit residues: 49.5194 Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 107 ASN C 224 ASN D 49 GLN D 224 ASN E 107 ASN E 224 ASN F 107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.055628 restraints weight = 41150.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057554 restraints weight = 20259.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058911 restraints weight = 12893.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059650 restraints weight = 9375.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060362 restraints weight = 7847.608| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10494 Z= 0.163 Angle : 0.739 10.053 14226 Z= 0.371 Chirality : 0.041 0.278 1602 Planarity : 0.004 0.027 1674 Dihedral : 9.338 59.919 1500 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.88 % Favored : 96.62 % Rotamer: Outliers : 4.44 % Allowed : 12.41 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.67 (0.24), residues: 1182 helix: 2.59 (0.18), residues: 828 sheet: 2.34 (0.68), residues: 66 loop : -0.97 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 189 TYR 0.011 0.001 TYR D 66 PHE 0.008 0.001 PHE E 199 TRP 0.002 0.000 TRP C 78 HIS 0.001 0.000 HIS F 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (10476) covalent geometry : angle 0.70483 / 0.36 (14190) SS BOND : bond 0.00970 / 0.64 ( 18) SS BOND : angle 4.48196 / 3.19 ( 36) hydrogen bonds : bond 0.04540 / 2.97 ( 702) hydrogen bonds : angle 3.01895 / 2.17 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.292 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: A 47 ASP cc_start: 0.8235 (p0) cc_final: 0.7943 (p0) REVERT: A 173 GLN cc_start: 0.9578 (tt0) cc_final: 0.8956 (tm-30) REVERT: B 92 TYR cc_start: 0.9260 (t80) cc_final: 0.8671 (t80) REVERT: B 173 GLN cc_start: 0.9591 (tt0) cc_final: 0.9006 (tm-30) REVERT: C 92 TYR cc_start: 0.9290 (t80) cc_final: 0.8585 (t80) REVERT: C 173 GLN cc_start: 0.9554 (tt0) cc_final: 0.9021 (tm-30) REVERT: D 47 ASP cc_start: 0.7973 (p0) cc_final: 0.7714 (p0) REVERT: D 103 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9166 (tp30) REVERT: D 155 TYR cc_start: 0.8551 (t80) cc_final: 0.8105 (t80) REVERT: D 173 GLN cc_start: 0.9634 (tt0) cc_final: 0.9065 (tm-30) REVERT: E 48 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: E 101 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8675 (tpt170) REVERT: E 173 GLN cc_start: 0.9565 (tt0) cc_final: 0.9066 (tm-30) REVERT: F 47 ASP cc_start: 0.8178 (p0) cc_final: 0.7928 (p0) REVERT: F 53 ARG cc_start: 0.8854 (ptp-110) cc_final: 0.8638 (mtm110) REVERT: F 101 ARG cc_start: 0.9032 (mtp85) cc_final: 0.8813 (tpt170) REVERT: F 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9017 (tm-30) outliers start: 48 outliers final: 35 residues processed: 220 average time/residue: 0.0918 time to fit residues: 28.4853 Evaluate side-chains 202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 0.0370 chunk 5 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN E 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.072717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057166 restraints weight = 42798.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059103 restraints weight = 20937.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060510 restraints weight = 13150.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061300 restraints weight = 9566.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061812 restraints weight = 7934.873| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10494 Z= 0.143 Angle : 0.719 11.748 14226 Z= 0.359 Chirality : 0.040 0.250 1602 Planarity : 0.004 0.031 1674 Dihedral : 9.077 58.998 1500 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.95 % Favored : 97.55 % Rotamer: Outliers : 4.07 % Allowed : 13.98 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.52 (0.24), residues: 1182 helix: 2.51 (0.18), residues: 834 sheet: 1.94 (0.71), residues: 66 loop : -1.13 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 189 TYR 0.010 0.001 TYR C 66 PHE 0.007 0.001 PHE D 32 TRP 0.002 0.000 TRP C 45 HIS 0.001 0.000 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (10476) covalent geometry : angle 0.69420 / 0.35 (14190) SS BOND : bond 0.00844 / 0.55 ( 18) SS BOND : angle 3.75136 / 2.63 ( 36) hydrogen bonds : bond 0.04365 / 2.87 ( 702) hydrogen bonds : angle 2.96643 / 2.12 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9553 (tt0) cc_final: 0.8957 (tm-30) REVERT: A 205 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8375 (mt-10) REVERT: B 92 TYR cc_start: 0.9222 (t80) cc_final: 0.8662 (t80) REVERT: B 173 GLN cc_start: 0.9570 (tt0) cc_final: 0.9014 (tm-30) REVERT: C 92 TYR cc_start: 0.9274 (t80) cc_final: 0.8591 (t80) REVERT: C 173 GLN cc_start: 0.9547 (tt0) cc_final: 0.8997 (tm-30) REVERT: D 103 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9231 (tp30) REVERT: D 155 TYR cc_start: 0.8599 (t80) cc_final: 0.8182 (t80) REVERT: E 101 ARG cc_start: 0.8970 (mtp85) cc_final: 0.8717 (tpt170) REVERT: E 173 GLN cc_start: 0.9548 (tt0) cc_final: 0.9042 (tm-30) REVERT: F 101 ARG cc_start: 0.9014 (mtp85) cc_final: 0.8765 (tpt170) REVERT: F 173 GLN cc_start: 0.9544 (tt0) cc_final: 0.9002 (tm-30) outliers start: 44 outliers final: 33 residues processed: 215 average time/residue: 0.0841 time to fit residues: 26.3126 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057241 restraints weight = 42627.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059200 restraints weight = 21113.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.060595 restraints weight = 13272.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.061470 restraints weight = 9699.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061863 restraints weight = 7877.049| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10494 Z= 0.141 Angle : 0.724 12.674 14226 Z= 0.361 Chirality : 0.039 0.231 1602 Planarity : 0.004 0.039 1674 Dihedral : 8.886 59.211 1500 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.62 % Favored : 96.87 % Rotamer: Outliers : 4.81 % Allowed : 15.00 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.38 (0.24), residues: 1182 helix: 2.48 (0.18), residues: 834 sheet: 1.60 (0.71), residues: 66 loop : -1.34 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.011 0.001 TYR B 66 PHE 0.007 0.001 PHE A 32 TRP 0.006 0.000 TRP F 45 HIS 0.003 0.001 HIS F 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10476) covalent geometry : angle 0.70417 / 0.35 (14190) SS BOND : bond 0.00908 / 0.61 ( 18) SS BOND : angle 3.43409 / 2.39 ( 36) hydrogen bonds : bond 0.04250 / 2.80 ( 702) hydrogen bonds : angle 3.00104 / 2.15 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9538 (tt0) cc_final: 0.8968 (tm-30) REVERT: B 42 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 92 TYR cc_start: 0.9242 (t80) cc_final: 0.8627 (t80) REVERT: B 173 GLN cc_start: 0.9564 (tt0) cc_final: 0.9047 (tm-30) REVERT: C 92 TYR cc_start: 0.9276 (t80) cc_final: 0.8588 (t80) REVERT: C 173 GLN cc_start: 0.9528 (tt0) cc_final: 0.9004 (tm-30) REVERT: D 103 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9207 (tp30) REVERT: D 155 TYR cc_start: 0.8625 (t80) cc_final: 0.8214 (t80) REVERT: E 101 ARG cc_start: 0.8962 (mtp85) cc_final: 0.8747 (tpt170) REVERT: E 173 GLN cc_start: 0.9534 (tt0) cc_final: 0.9048 (tm-30) REVERT: F 173 GLN cc_start: 0.9529 (tt0) cc_final: 0.9011 (tm-30) outliers start: 52 outliers final: 37 residues processed: 221 average time/residue: 0.0825 time to fit residues: 26.5022 Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057340 restraints weight = 42293.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059296 restraints weight = 21210.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060717 restraints weight = 13418.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061475 restraints weight = 9787.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062178 restraints weight = 8125.745| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10494 Z= 0.135 Angle : 0.731 11.708 14226 Z= 0.360 Chirality : 0.039 0.240 1602 Planarity : 0.004 0.037 1674 Dihedral : 8.694 59.492 1500 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.45 % Favored : 97.04 % Rotamer: Outliers : 4.17 % Allowed : 18.06 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.40 (0.24), residues: 1182 helix: 2.48 (0.17), residues: 846 sheet: 1.30 (0.71), residues: 66 loop : -1.40 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.009 0.001 TYR C 66 PHE 0.008 0.001 PHE A 32 TRP 0.028 0.001 TRP F 45 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10476) covalent geometry : angle 0.71409 / 0.35 (14190) SS BOND : bond 0.00891 / 0.59 ( 18) SS BOND : angle 3.19911 / 2.23 ( 36) hydrogen bonds : bond 0.04097 / 2.72 ( 702) hydrogen bonds : angle 3.00728 / 2.15 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.9316 (tp30) cc_final: 0.8957 (tp30) REVERT: A 173 GLN cc_start: 0.9512 (tt0) cc_final: 0.8987 (tm-30) REVERT: B 92 TYR cc_start: 0.9234 (t80) cc_final: 0.8674 (t80) REVERT: B 173 GLN cc_start: 0.9544 (tt0) cc_final: 0.9048 (tm-30) REVERT: B 205 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 173 GLN cc_start: 0.9516 (tt0) cc_final: 0.9025 (tm-30) REVERT: D 92 TYR cc_start: 0.9412 (t80) cc_final: 0.9187 (t80) REVERT: D 155 TYR cc_start: 0.8631 (t80) cc_final: 0.8278 (t80) REVERT: D 173 GLN cc_start: 0.9565 (tt0) cc_final: 0.9073 (tm-30) REVERT: E 42 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8327 (tm-30) REVERT: E 173 GLN cc_start: 0.9520 (tt0) cc_final: 0.9083 (tm-30) REVERT: F 173 GLN cc_start: 0.9524 (tt0) cc_final: 0.9020 (tm-30) outliers start: 45 outliers final: 35 residues processed: 215 average time/residue: 0.0803 time to fit residues: 25.4564 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054348 restraints weight = 44291.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.056188 restraints weight = 22517.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057487 restraints weight = 14500.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058387 restraints weight = 10800.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058934 restraints weight = 8778.283| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10494 Z= 0.219 Angle : 0.758 11.697 14226 Z= 0.384 Chirality : 0.040 0.213 1602 Planarity : 0.004 0.044 1674 Dihedral : 8.662 59.546 1500 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.72 % Allowed : 17.69 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.22 (0.24), residues: 1182 helix: 2.38 (0.17), residues: 834 sheet: 1.63 (0.70), residues: 60 loop : -1.43 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.011 0.001 TYR A 92 PHE 0.011 0.001 PHE A 169 TRP 0.035 0.001 TRP C 45 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (10476) covalent geometry : angle 0.73812 / 0.38 (14190) SS BOND : bond 0.00774 / 0.51 ( 18) SS BOND : angle 3.48780 / 2.45 ( 36) hydrogen bonds : bond 0.04667 / 3.08 ( 702) hydrogen bonds : angle 3.20079 / 2.30 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9595 (tt0) cc_final: 0.9060 (tm-30) REVERT: A 205 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8673 (pm20) REVERT: B 92 TYR cc_start: 0.9308 (t80) cc_final: 0.8701 (t80) REVERT: B 173 GLN cc_start: 0.9615 (tt0) cc_final: 0.9087 (tm-30) REVERT: C 173 GLN cc_start: 0.9598 (tt0) cc_final: 0.9035 (tm-30) REVERT: C 195 GLN cc_start: 0.9245 (mt0) cc_final: 0.8767 (pp30) REVERT: D 205 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8565 (mt-10) REVERT: E 173 GLN cc_start: 0.9591 (tt0) cc_final: 0.9088 (tm-30) REVERT: F 173 GLN cc_start: 0.9597 (tt0) cc_final: 0.9033 (tm-30) outliers start: 51 outliers final: 38 residues processed: 203 average time/residue: 0.0819 time to fit residues: 24.3285 Evaluate side-chains 188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN D 224 ASN E 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056216 restraints weight = 43383.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058120 restraints weight = 22085.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059446 restraints weight = 14243.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060381 restraints weight = 10518.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060985 restraints weight = 8538.207| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10494 Z= 0.137 Angle : 0.741 10.863 14226 Z= 0.366 Chirality : 0.039 0.205 1602 Planarity : 0.004 0.054 1674 Dihedral : 8.406 59.626 1498 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.07 % Allowed : 18.24 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.22 (0.24), residues: 1182 helix: 2.44 (0.18), residues: 834 sheet: 1.48 (0.73), residues: 60 loop : -1.60 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 53 TYR 0.008 0.001 TYR C 66 PHE 0.008 0.001 PHE A 32 TRP 0.018 0.001 TRP C 45 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10476) covalent geometry : angle 0.72631 / 0.36 (14190) SS BOND : bond 0.00867 / 0.56 ( 18) SS BOND : angle 2.96290 / 2.02 ( 36) hydrogen bonds : bond 0.04326 / 2.86 ( 702) hydrogen bonds : angle 3.08593 / 2.22 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9536 (tt0) cc_final: 0.9045 (tm-30) REVERT: A 195 GLN cc_start: 0.9209 (mt0) cc_final: 0.8654 (pp30) REVERT: B 42 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 92 TYR cc_start: 0.9272 (t80) cc_final: 0.8674 (t80) REVERT: B 173 GLN cc_start: 0.9579 (tt0) cc_final: 0.9081 (tm-30) REVERT: C 166 GLU cc_start: 0.8877 (pp20) cc_final: 0.8652 (pp20) REVERT: C 173 GLN cc_start: 0.9530 (tt0) cc_final: 0.9017 (tm-30) REVERT: C 195 GLN cc_start: 0.9181 (mt0) cc_final: 0.8731 (pp30) REVERT: D 155 TYR cc_start: 0.8810 (t80) cc_final: 0.8522 (t80) REVERT: D 195 GLN cc_start: 0.9194 (mt0) cc_final: 0.8531 (pp30) REVERT: D 205 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8483 (mt-10) REVERT: E 42 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8337 (tm-30) REVERT: E 173 GLN cc_start: 0.9535 (tt0) cc_final: 0.9064 (tm-30) REVERT: E 205 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8451 (mt-10) REVERT: F 173 GLN cc_start: 0.9531 (tt0) cc_final: 0.9023 (tm-30) REVERT: F 195 GLN cc_start: 0.9160 (mt0) cc_final: 0.8776 (pp30) outliers start: 44 outliers final: 36 residues processed: 207 average time/residue: 0.0827 time to fit residues: 25.1122 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057015 restraints weight = 43112.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058944 restraints weight = 21785.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060188 restraints weight = 14026.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061158 restraints weight = 10532.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061819 restraints weight = 8487.377| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10494 Z= 0.133 Angle : 0.739 11.286 14226 Z= 0.365 Chirality : 0.039 0.193 1602 Planarity : 0.004 0.048 1674 Dihedral : 8.276 59.532 1498 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.17 % Allowed : 18.33 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.13 (0.24), residues: 1182 helix: 2.37 (0.17), residues: 834 sheet: 1.63 (0.75), residues: 60 loop : -1.66 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 53 TYR 0.005 0.001 TYR C 66 PHE 0.008 0.001 PHE F 32 TRP 0.017 0.001 TRP C 45 HIS 0.002 0.000 HIS D 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10476) covalent geometry : angle 0.72792 / 0.36 (14190) SS BOND : bond 0.00860 / 0.56 ( 18) SS BOND : angle 2.58305 / 1.73 ( 36) hydrogen bonds : bond 0.04140 / 2.74 ( 702) hydrogen bonds : angle 3.10866 / 2.23 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8634 (t80) cc_final: 0.8422 (t80) REVERT: A 173 GLN cc_start: 0.9495 (tt0) cc_final: 0.9055 (tm-30) REVERT: A 195 GLN cc_start: 0.9238 (mt0) cc_final: 0.8586 (pp30) REVERT: B 92 TYR cc_start: 0.9271 (t80) cc_final: 0.8679 (t80) REVERT: B 173 GLN cc_start: 0.9531 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 173 GLN cc_start: 0.9494 (tt0) cc_final: 0.9030 (tm-30) REVERT: C 195 GLN cc_start: 0.9175 (mt0) cc_final: 0.8727 (pp30) REVERT: D 155 TYR cc_start: 0.8752 (t80) cc_final: 0.8477 (t80) REVERT: D 173 GLN cc_start: 0.9536 (tt0) cc_final: 0.9119 (tm-30) REVERT: D 195 GLN cc_start: 0.9201 (mt0) cc_final: 0.8417 (pp30) REVERT: D 205 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8456 (mt-10) REVERT: E 42 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8386 (tm-30) REVERT: E 173 GLN cc_start: 0.9503 (tt0) cc_final: 0.9103 (tm-30) REVERT: E 195 GLN cc_start: 0.9135 (mt0) cc_final: 0.8791 (pp30) REVERT: E 205 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8521 (mt-10) REVERT: F 92 TYR cc_start: 0.9125 (t80) cc_final: 0.8728 (t80) REVERT: F 173 GLN cc_start: 0.9500 (tt0) cc_final: 0.9033 (tm-30) REVERT: F 195 GLN cc_start: 0.9109 (mt0) cc_final: 0.8780 (pp30) outliers start: 45 outliers final: 35 residues processed: 211 average time/residue: 0.0874 time to fit residues: 27.0704 Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 119 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 224 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 = 0.3406 r_free = 0.3406 target = 0.071878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056200 restraints weight = 42925.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058151 restraints weight = 21666.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059518 restraints weight = 13879.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060388 restraints weight = 10093.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060951 restraints weight = 8224.286| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10494 Z= 0.144 Angle : 0.754 10.156 14226 Z= 0.375 Chirality : 0.039 0.185 1602 Planarity : 0.004 0.064 1674 Dihedral : 8.185 59.446 1498 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 19.44 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.15 (0.24), residues: 1182 helix: 2.37 (0.18), residues: 834 sheet: 1.68 (0.75), residues: 60 loop : -1.61 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 53 TYR 0.007 0.001 TYR B 66 PHE 0.007 0.001 PHE F 32 TRP 0.016 0.001 TRP C 45 HIS 0.001 0.000 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (10476) covalent geometry : angle 0.74236 / 0.37 (14190) SS BOND : bond 0.00809 / 0.53 ( 18) SS BOND : angle 2.71343 / 1.83 ( 36) hydrogen bonds : bond 0.04180 / 2.77 ( 702) hydrogen bonds : angle 3.12730 / 2.25 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9065 (tm-30) REVERT: A 195 GLN cc_start: 0.9206 (mt0) cc_final: 0.8642 (pp30) REVERT: B 92 TYR cc_start: 0.9281 (t80) cc_final: 0.8696 (t80) REVERT: B 173 GLN cc_start: 0.9552 (tt0) cc_final: 0.9075 (tm-30) REVERT: B 195 GLN cc_start: 0.9097 (mt0) cc_final: 0.8489 (pp30) REVERT: C 173 GLN cc_start: 0.9509 (tt0) cc_final: 0.9039 (tm-30) REVERT: C 195 GLN cc_start: 0.9148 (mt0) cc_final: 0.8612 (pp30) REVERT: D 47 ASP cc_start: 0.8077 (p0) cc_final: 0.7842 (p0) REVERT: D 155 TYR cc_start: 0.8843 (t80) cc_final: 0.8488 (t80) REVERT: D 173 GLN cc_start: 0.9547 (tt0) cc_final: 0.9116 (tm-30) REVERT: D 195 GLN cc_start: 0.9194 (mt0) cc_final: 0.8530 (pp30) REVERT: D 205 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8501 (mt-10) REVERT: E 173 GLN cc_start: 0.9518 (tt0) cc_final: 0.9100 (tm-30) REVERT: E 195 GLN cc_start: 0.9110 (mt0) cc_final: 0.8719 (pp30) REVERT: E 205 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8493 (mt-10) REVERT: F 173 GLN cc_start: 0.9514 (tt0) cc_final: 0.9047 (tm-30) REVERT: F 195 GLN cc_start: 0.9105 (mt0) cc_final: 0.8783 (pp30) outliers start: 36 outliers final: 35 residues processed: 200 average time/residue: 0.0865 time to fit residues: 25.2423 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057539 restraints weight = 42985.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059476 restraints weight = 22050.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060858 restraints weight = 14274.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.061716 restraints weight = 10463.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062237 restraints weight = 8595.810| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10494 Z= 0.137 Angle : 0.761 9.838 14226 Z= 0.377 Chirality : 0.039 0.179 1602 Planarity : 0.004 0.042 1674 Dihedral : 8.043 59.693 1498 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.52 % Allowed : 19.17 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.10 (0.24), residues: 1182 helix: 2.35 (0.18), residues: 834 sheet: 1.55 (0.76), residues: 60 loop : -1.68 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.005 0.001 TYR C 66 PHE 0.008 0.001 PHE F 32 TRP 0.014 0.001 TRP C 45 HIS 0.001 0.000 HIS E 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10476) covalent geometry : angle 0.75182 / 0.37 (14190) SS BOND : bond 0.00782 / 0.51 ( 18) SS BOND : angle 2.44963 / 1.63 ( 36) hydrogen bonds : bond 0.04056 / 2.69 ( 702) hydrogen bonds : angle 3.15343 / 2.27 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9478 (tt0) cc_final: 0.9069 (tm-30) REVERT: A 195 GLN cc_start: 0.9092 (mt0) cc_final: 0.8612 (pp30) REVERT: B 92 TYR cc_start: 0.9252 (t80) cc_final: 0.8680 (t80) REVERT: B 173 GLN cc_start: 0.9516 (tt0) cc_final: 0.9075 (tm-30) REVERT: B 195 GLN cc_start: 0.9094 (mt0) cc_final: 0.8462 (pp30) REVERT: C 92 TYR cc_start: 0.9216 (t80) cc_final: 0.8849 (t80) REVERT: C 173 GLN cc_start: 0.9471 (tt0) cc_final: 0.9054 (tm-30) REVERT: C 195 GLN cc_start: 0.9057 (mt0) cc_final: 0.8560 (pp30) REVERT: D 42 GLU cc_start: 0.8580 (pp20) cc_final: 0.8165 (pt0) REVERT: D 155 TYR cc_start: 0.8780 (t80) cc_final: 0.8372 (t80) REVERT: D 173 GLN cc_start: 0.9513 (tt0) cc_final: 0.9141 (tm-30) REVERT: D 195 GLN cc_start: 0.9152 (mt0) cc_final: 0.8520 (pp30) REVERT: D 205 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 92 TYR cc_start: 0.9092 (t80) cc_final: 0.8751 (t80) REVERT: E 173 GLN cc_start: 0.9482 (tt0) cc_final: 0.9119 (tm-30) REVERT: E 195 GLN cc_start: 0.9070 (mt0) cc_final: 0.8714 (pp30) REVERT: E 205 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8489 (mt-10) REVERT: F 92 TYR cc_start: 0.9143 (t80) cc_final: 0.8756 (t80) REVERT: F 173 GLN cc_start: 0.9473 (tt0) cc_final: 0.9049 (tm-30) REVERT: F 195 GLN cc_start: 0.9076 (mt0) cc_final: 0.8842 (pp30) outliers start: 38 outliers final: 30 residues processed: 205 average time/residue: 0.0870 time to fit residues: 26.1559 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 11 optimal weight: 0.0670 chunk 31 optimal weight: 9.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.072779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057167 restraints weight = 43127.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059134 restraints weight = 21562.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060336 restraints weight = 13673.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061326 restraints weight = 10403.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061936 restraints weight = 8322.147| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 10494 Z= 0.206 Angle : 0.987 59.198 14226 Z= 0.556 Chirality : 0.046 0.945 1602 Planarity : 0.004 0.063 1674 Dihedral : 7.797 59.688 1488 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 3.15 % Allowed : 19.91 % Favored : 76.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 2.05 (0.24), residues: 1182 helix: 2.32 (0.18), residues: 834 sheet: 1.52 (0.76), residues: 60 loop : -1.70 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.007 0.001 TYR C 66 PHE 0.008 0.001 PHE F 32 TRP 0.013 0.001 TRP C 45 HIS 0.001 0.000 HIS D 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (10476) covalent geometry : angle 0.97936 / 0.55 (14190) SS BOND : bond 0.00835 / 0.55 ( 18) SS BOND : angle 2.69768 / 1.74 ( 36) hydrogen bonds : bond 0.04162 / 2.72 ( 702) hydrogen bonds : angle 3.18891 / 2.31 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.88 seconds wall clock time: 27 minutes 23.27 seconds (1643.27 seconds total)