Starting phenix.real_space_refine on Sun Apr 5 04:14:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.map" model { file = "/net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uww_64566/04_2026/9uww_64566.cif" } resolution = 2.19 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= -0.001 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 42 5.16 5 Na 1 4.78 5 C 5103 2.51 5 N 1299 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7924 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2580 Classifications: {'peptide': 329} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 313} Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2580 Classifications: {'peptide': 329} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 313} Chain: "C" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2580 Classifications: {'peptide': 329} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 313} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' NA': 1, 'NAG': 2, 'PG8': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'NAG': 2, 'PG8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'NAG': 2, 'PG8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.03, per 1000 atoms: 0.26 Number of scatterers: 7924 At special positions: 0 Unit cell: (86.45, 91.2, 124.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Na 1 11.00 O 1476 8.00 N 1299 7.00 C 5103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 194 " " NAG A 502 " - " ASN A 133 " " NAG B 501 " - " ASN B 194 " " NAG B 502 " - " ASN B 133 " " NAG C 501 " - " ASN C 194 " " NAG C 502 " - " ASN C 133 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 320.3 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 26.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 39 through 60 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.569A pdb=" N TYR A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.568A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.530A pdb=" N CYS A 279 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.767A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.568A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.568A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.531A pdb=" N CYS B 279 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 366 removed outlier: 3.766A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 60 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.570A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.569A pdb=" N LEU C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.530A pdb=" N CYS C 279 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 366 removed outlier: 3.765A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 removed outlier: 3.684A pdb=" N PHE A 210 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.683A pdb=" N LYS A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 removed outlier: 3.684A pdb=" N PHE B 210 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.683A pdb=" N LYS B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 removed outlier: 3.685A pdb=" N PHE C 210 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 removed outlier: 3.682A pdb=" N LYS C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 570 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: 1.35 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1790 1.33 - 1.45: 1815 1.45 - 1.57: 4456 1.57 - 1.70: 6 1.70 - 1.82: 51 Bond restraints: 8118 Sorted by residual: bond pdb=" C15 PG8 C 503 " pdb=" O9 PG8 C 503 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C15 PG8 A 503 " pdb=" O9 PG8 A 503 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C15 PG8 B 503 " pdb=" O9 PG8 B 503 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C7 PG8 A 503 " pdb=" O7 PG8 A 503 " ideal model delta sigma weight residual 1.336 1.453 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C7 PG8 C 503 " pdb=" O7 PG8 C 503 " ideal model delta sigma weight residual 1.336 1.453 -0.117 2.00e-02 2.50e+03 3.39e+01 ... (remaining 8113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10728 1.89 - 3.78: 229 3.78 - 5.67: 32 5.67 - 7.57: 3 7.57 - 9.46: 12 Bond angle restraints: 11004 Sorted by residual: angle pdb=" C8 PG8 C 503 " pdb=" C7 PG8 C 503 " pdb=" O7 PG8 C 503 " ideal model delta sigma weight residual 110.93 120.39 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C8 PG8 B 503 " pdb=" C7 PG8 B 503 " pdb=" O7 PG8 B 503 " ideal model delta sigma weight residual 110.93 120.34 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" C8 PG8 A 503 " pdb=" C7 PG8 A 503 " pdb=" O7 PG8 A 503 " ideal model delta sigma weight residual 110.93 120.33 -9.40 3.00e+00 1.11e-01 9.83e+00 angle pdb=" O3 PG8 C 503 " pdb=" P1 PG8 C 503 " pdb=" O6 PG8 C 503 " ideal model delta sigma weight residual 93.78 103.10 -9.32 3.00e+00 1.11e-01 9.64e+00 angle pdb=" O3 PG8 B 503 " pdb=" P1 PG8 B 503 " pdb=" O6 PG8 B 503 " ideal model delta sigma weight residual 93.78 103.08 -9.30 3.00e+00 1.11e-01 9.60e+00 ... (remaining 10999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4506 16.92 - 33.85: 312 33.85 - 50.77: 63 50.77 - 67.70: 12 67.70 - 84.62: 18 Dihedral angle restraints: 4911 sinusoidal: 2076 harmonic: 2835 Sorted by residual: dihedral pdb=" CA LYS A 207 " pdb=" C LYS A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LYS C 207 " pdb=" C LYS C 207 " pdb=" N PHE C 208 " pdb=" CA PHE C 208 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LYS B 207 " pdb=" C LYS B 207 " pdb=" N PHE B 208 " pdb=" CA PHE B 208 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 938 0.053 - 0.106: 240 0.106 - 0.160: 58 0.160 - 0.213: 3 0.213 - 0.266: 3 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C2 PG8 B 503 " pdb=" C1 PG8 B 503 " pdb=" C3 PG8 B 503 " pdb=" O5 PG8 B 503 " both_signs ideal model delta sigma weight residual False -2.29 -2.56 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2 PG8 A 503 " pdb=" C1 PG8 A 503 " pdb=" C3 PG8 A 503 " pdb=" O5 PG8 A 503 " both_signs ideal model delta sigma weight residual False -2.29 -2.56 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 PG8 C 503 " pdb=" C1 PG8 C 503 " pdb=" C3 PG8 C 503 " pdb=" O5 PG8 C 503 " both_signs ideal model delta sigma weight residual False -2.29 -2.56 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1239 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 58 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C TRP A 58 " -0.032 2.00e-02 2.50e+03 pdb=" O TRP A 58 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 59 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 58 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C TRP C 58 " 0.032 2.00e-02 2.50e+03 pdb=" O TRP C 58 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR C 59 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 58 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C TRP B 58 " 0.031 2.00e-02 2.50e+03 pdb=" O TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 59 " -0.011 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3584 2.95 - 3.44: 6986 3.44 - 3.92: 12519 3.92 - 4.41: 14555 4.41 - 4.90: 23862 Nonbonded interactions: 61506 Sorted by model distance: nonbonded pdb=" NZ LYS C 212 " pdb=" O CYS C 279 " model vdw 2.461 3.120 nonbonded pdb=" NZ LYS B 212 " pdb=" O CYS B 279 " model vdw 2.462 3.120 nonbonded pdb=" NZ LYS A 212 " pdb=" O CYS A 279 " model vdw 2.462 3.120 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.481 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.482 3.040 ... (remaining 61501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 503) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 8139 Z= 0.275 Angle : 0.727 9.457 11052 Z= 0.368 Chirality : 0.051 0.266 1242 Planarity : 0.005 0.040 1371 Dihedral : 13.234 84.624 3060 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.24), residues: 981 helix: -1.02 (0.28), residues: 234 sheet: 0.31 (0.25), residues: 309 loop : -1.50 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.017 0.002 TYR B 45 PHE 0.011 0.002 PHE B 303 TRP 0.012 0.002 TRP B 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 8118) covalent geometry : angle 0.72127 (11004) SS BOND : bond 0.00178 ( 15) SS BOND : angle 1.09136 ( 30) hydrogen bonds : bond 0.11780 ( 211) hydrogen bonds : angle 5.08470 ( 570) link_NAG-ASN : bond 0.00363 ( 6) link_NAG-ASN : angle 2.21446 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.303 Fit side-chains REVERT: B 230 GLU cc_start: 0.8470 (pt0) cc_final: 0.8263 (pm20) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.6582 time to fit residues: 57.4778 Evaluate side-chains 63 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 310 ASN B 152 ASN B 310 ASN C 49 GLN C 152 ASN C 310 ASN C 332 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.060126 restraints weight = 13782.101| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.44 r_work: 0.2665 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8139 Z= 0.090 Angle : 0.480 5.543 11052 Z= 0.257 Chirality : 0.046 0.176 1242 Planarity : 0.004 0.032 1371 Dihedral : 7.514 66.587 1287 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.53 % Allowed : 6.48 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 981 helix: 0.62 (0.33), residues: 234 sheet: 0.58 (0.24), residues: 345 loop : -0.87 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.008 0.001 TYR A 222 PHE 0.006 0.001 PHE A 303 TRP 0.005 0.001 TRP A 93 HIS 0.002 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8118) covalent geometry : angle 0.47701 (11004) SS BOND : bond 0.00335 ( 15) SS BOND : angle 0.69444 ( 30) hydrogen bonds : bond 0.04330 ( 211) hydrogen bonds : angle 4.74470 ( 570) link_NAG-ASN : bond 0.00364 ( 6) link_NAG-ASN : angle 1.26440 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.305 Fit side-chains REVERT: A 246 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8887 (tm-30) REVERT: B 230 GLU cc_start: 0.9349 (pt0) cc_final: 0.8692 (pm20) REVERT: C 258 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9305 (mtpt) outliers start: 13 outliers final: 1 residues processed: 81 average time/residue: 0.5327 time to fit residues: 46.0683 Evaluate side-chains 69 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 49 GLN B 201 ASN C 49 GLN C 201 ASN C 310 ASN C 332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.058246 restraints weight = 13586.752| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.44 r_work: 0.2618 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8139 Z= 0.119 Angle : 0.492 5.412 11052 Z= 0.264 Chirality : 0.046 0.171 1242 Planarity : 0.004 0.034 1371 Dihedral : 7.495 66.358 1287 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.24 % Allowed : 7.66 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 981 helix: 1.46 (0.36), residues: 234 sheet: 0.83 (0.24), residues: 345 loop : -0.66 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.012 0.001 TYR C 45 PHE 0.008 0.001 PHE B 243 TRP 0.008 0.001 TRP A 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8118) covalent geometry : angle 0.48626 (11004) SS BOND : bond 0.00336 ( 15) SS BOND : angle 0.92443 ( 30) hydrogen bonds : bond 0.04600 ( 211) hydrogen bonds : angle 4.67349 ( 570) link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 1.57059 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.319 Fit side-chains REVERT: A 246 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8867 (tm-30) REVERT: B 230 GLU cc_start: 0.9370 (pt0) cc_final: 0.8727 (pm20) REVERT: C 258 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9368 (mtpt) outliers start: 19 outliers final: 8 residues processed: 75 average time/residue: 0.5522 time to fit residues: 44.1346 Evaluate side-chains 75 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.059843 restraints weight = 13805.191| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.47 r_work: 0.2658 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8139 Z= 0.087 Angle : 0.447 5.349 11052 Z= 0.238 Chirality : 0.045 0.172 1242 Planarity : 0.003 0.030 1371 Dihedral : 7.283 65.723 1287 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.41 % Allowed : 9.07 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 981 helix: 1.82 (0.37), residues: 234 sheet: 1.04 (0.24), residues: 351 loop : -0.38 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.008 0.001 TYR C 98 PHE 0.006 0.001 PHE C 303 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 8118) covalent geometry : angle 0.44328 (11004) SS BOND : bond 0.00281 ( 15) SS BOND : angle 0.73029 ( 30) hydrogen bonds : bond 0.03898 ( 211) hydrogen bonds : angle 4.51668 ( 570) link_NAG-ASN : bond 0.00341 ( 6) link_NAG-ASN : angle 1.32035 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.307 Fit side-chains REVERT: B 230 GLU cc_start: 0.9355 (pt0) cc_final: 0.8767 (pm20) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.5449 time to fit residues: 42.3853 Evaluate side-chains 75 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 310 ASN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.056390 restraints weight = 13761.933| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.46 r_work: 0.2581 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8139 Z= 0.188 Angle : 0.543 5.552 11052 Z= 0.296 Chirality : 0.048 0.166 1242 Planarity : 0.004 0.035 1371 Dihedral : 7.576 65.138 1287 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.59 % Allowed : 7.77 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 981 helix: 1.76 (0.37), residues: 234 sheet: 0.99 (0.24), residues: 345 loop : -0.41 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.010 0.002 TYR C 98 PHE 0.011 0.001 PHE B 243 TRP 0.011 0.001 TRP B 268 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8118) covalent geometry : angle 0.53470 (11004) SS BOND : bond 0.00378 ( 15) SS BOND : angle 1.14565 ( 30) hydrogen bonds : bond 0.05268 ( 211) hydrogen bonds : angle 4.74047 ( 570) link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 2.01047 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.324 Fit side-chains REVERT: B 44 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8787 (tt) REVERT: B 230 GLU cc_start: 0.9363 (pt0) cc_final: 0.8717 (pm20) REVERT: C 258 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9322 (mtpt) outliers start: 22 outliers final: 12 residues processed: 76 average time/residue: 0.5459 time to fit residues: 44.1709 Evaluate side-chains 78 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.0030 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 310 ASN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058341 restraints weight = 13585.162| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.45 r_work: 0.2625 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8139 Z= 0.105 Angle : 0.469 5.407 11052 Z= 0.253 Chirality : 0.046 0.169 1242 Planarity : 0.004 0.035 1371 Dihedral : 7.325 64.573 1287 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.94 % Allowed : 7.54 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 981 helix: 1.82 (0.37), residues: 234 sheet: 1.13 (0.24), residues: 345 loop : -0.22 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.008 0.001 TYR A 222 PHE 0.006 0.001 PHE C 303 TRP 0.008 0.001 TRP A 268 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8118) covalent geometry : angle 0.46375 (11004) SS BOND : bond 0.00310 ( 15) SS BOND : angle 0.81479 ( 30) hydrogen bonds : bond 0.04349 ( 211) hydrogen bonds : angle 4.58723 ( 570) link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 1.54822 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.349 Fit side-chains REVERT: B 44 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8784 (tt) REVERT: B 230 GLU cc_start: 0.9376 (pt0) cc_final: 0.8753 (pm20) outliers start: 25 outliers final: 10 residues processed: 76 average time/residue: 0.5541 time to fit residues: 44.7543 Evaluate side-chains 76 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 310 ASN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.058271 restraints weight = 13739.547| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.46 r_work: 0.2624 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8139 Z= 0.111 Angle : 0.472 5.408 11052 Z= 0.255 Chirality : 0.046 0.167 1242 Planarity : 0.004 0.035 1371 Dihedral : 7.289 64.779 1287 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.71 % Allowed : 8.01 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 981 helix: 1.83 (0.37), residues: 234 sheet: 1.21 (0.24), residues: 345 loop : -0.15 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.008 0.001 TYR C 98 PHE 0.007 0.001 PHE B 243 TRP 0.008 0.001 TRP A 268 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8118) covalent geometry : angle 0.46671 (11004) SS BOND : bond 0.00275 ( 15) SS BOND : angle 0.84580 ( 30) hydrogen bonds : bond 0.04338 ( 211) hydrogen bonds : angle 4.58109 ( 570) link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 1.59209 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.248 Fit side-chains REVERT: A 130 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8518 (mtm110) REVERT: B 44 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 230 GLU cc_start: 0.9370 (pt0) cc_final: 0.8762 (pm20) outliers start: 23 outliers final: 11 residues processed: 77 average time/residue: 0.5331 time to fit residues: 43.8281 Evaluate side-chains 79 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.058897 restraints weight = 13807.814| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.46 r_work: 0.2635 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8139 Z= 0.099 Angle : 0.455 5.399 11052 Z= 0.245 Chirality : 0.045 0.168 1242 Planarity : 0.003 0.033 1371 Dihedral : 7.224 65.239 1287 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 8.83 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 981 helix: 1.86 (0.37), residues: 234 sheet: 1.27 (0.25), residues: 345 loop : -0.06 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 130 TYR 0.008 0.001 TYR A 222 PHE 0.006 0.001 PHE B 243 TRP 0.007 0.001 TRP A 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8118) covalent geometry : angle 0.45063 (11004) SS BOND : bond 0.00257 ( 15) SS BOND : angle 0.78182 ( 30) hydrogen bonds : bond 0.04104 ( 211) hydrogen bonds : angle 4.53238 ( 570) link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 1.47790 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.304 Fit side-chains REVERT: A 130 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8595 (mtm110) REVERT: B 44 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8775 (tt) REVERT: B 69 GLU cc_start: 0.8803 (tt0) cc_final: 0.8538 (pt0) REVERT: B 230 GLU cc_start: 0.9373 (pt0) cc_final: 0.8766 (pm20) outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.5040 time to fit residues: 41.5609 Evaluate side-chains 80 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057731 restraints weight = 13666.716| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.46 r_work: 0.2612 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8139 Z= 0.129 Angle : 0.491 5.440 11052 Z= 0.265 Chirality : 0.046 0.165 1242 Planarity : 0.004 0.035 1371 Dihedral : 7.307 65.549 1287 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.12 % Allowed : 8.72 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 981 helix: 1.83 (0.37), residues: 234 sheet: 1.23 (0.25), residues: 345 loop : -0.11 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.009 0.001 TYR A 222 PHE 0.008 0.001 PHE B 243 TRP 0.008 0.001 TRP B 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8118) covalent geometry : angle 0.48505 (11004) SS BOND : bond 0.00295 ( 15) SS BOND : angle 0.91461 ( 30) hydrogen bonds : bond 0.04535 ( 211) hydrogen bonds : angle 4.59865 ( 570) link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 1.68413 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.385 Fit side-chains REVERT: A 130 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8589 (mtm110) REVERT: B 44 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8771 (tt) REVERT: B 69 GLU cc_start: 0.8816 (tt0) cc_final: 0.8535 (pt0) REVERT: B 230 GLU cc_start: 0.9370 (pt0) cc_final: 0.8759 (pm20) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.5500 time to fit residues: 43.4019 Evaluate side-chains 81 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058377 restraints weight = 13512.090| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.45 r_work: 0.2627 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8139 Z= 0.110 Angle : 0.472 5.709 11052 Z= 0.255 Chirality : 0.045 0.166 1242 Planarity : 0.004 0.034 1371 Dihedral : 7.245 65.938 1287 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 9.07 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 981 helix: 1.85 (0.37), residues: 234 sheet: 1.27 (0.25), residues: 345 loop : -0.04 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 130 TYR 0.008 0.001 TYR A 222 PHE 0.007 0.001 PHE B 243 TRP 0.007 0.001 TRP A 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8118) covalent geometry : angle 0.46728 (11004) SS BOND : bond 0.00271 ( 15) SS BOND : angle 0.82556 ( 30) hydrogen bonds : bond 0.04280 ( 211) hydrogen bonds : angle 4.55830 ( 570) link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 1.56385 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.330 Fit side-chains REVERT: A 130 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8586 (mtm110) REVERT: B 44 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 69 GLU cc_start: 0.8807 (tt0) cc_final: 0.8536 (pt0) REVERT: B 230 GLU cc_start: 0.9370 (pt0) cc_final: 0.8763 (pm20) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.5387 time to fit residues: 42.0676 Evaluate side-chains 77 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN C 310 ASN C 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057519 restraints weight = 13593.136| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.45 r_work: 0.2605 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8139 Z= 0.140 Angle : 0.503 5.468 11052 Z= 0.272 Chirality : 0.046 0.163 1242 Planarity : 0.004 0.035 1371 Dihedral : 7.336 66.314 1287 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.36 % Allowed : 8.60 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 981 helix: 1.82 (0.37), residues: 234 sheet: 1.21 (0.25), residues: 345 loop : -0.10 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 130 TYR 0.009 0.001 TYR C 98 PHE 0.008 0.001 PHE B 243 TRP 0.009 0.001 TRP B 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8118) covalent geometry : angle 0.49688 (11004) SS BOND : bond 0.00310 ( 15) SS BOND : angle 0.94586 ( 30) hydrogen bonds : bond 0.04681 ( 211) hydrogen bonds : angle 4.62378 ( 570) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 1.75395 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.57 seconds wall clock time: 65 minutes 8.14 seconds (3908.14 seconds total)