Starting phenix.real_space_refine on Sat May 2 15:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.map" model { file = "/net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wno_66120/05_2026/9wno_66120.cif" } resolution = 3.48 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= 0.004 sd= 0.088 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 1 5.49 5 S 27 5.16 5 C 4492 2.51 5 N 1074 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6818 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3379 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3298 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 20, 'TRANS': 386} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'MJC': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'MJC:plan-1': 1, 'MJC:plan-2': 1, 'MJC:plan-3': 1, 'MJC:plan-4': 1, 'MJC:plan-5': 1, 'MJC:plan-6': 1, 'MJC:plan-8': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.90, per 1000 atoms: 0.28 Number of scatterers: 6818 At special positions: 0 Unit cell: (80.512, 70.72, 138.176, 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 27 16.00 P 1 15.00 O 1224 8.00 N 1074 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 198 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 501 " - " ASN B 35 " " NAG C 1 " - " ASN B 365 " " NAG D 1 " - " ASN B 319 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 388.4 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 48.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.503A pdb=" N GLN A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.281A pdb=" N SER A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 82 through 108 removed outlier: 3.696A pdb=" N SER A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.033A pdb=" N TRP A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 139 through 156 removed outlier: 3.572A pdb=" N LEU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.664A pdb=" N ILE A 177 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.642A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 removed outlier: 3.559A pdb=" N SER A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP A 229 " --> pdb=" O MET A 225 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 252 through 262 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.885A pdb=" N LYS A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.510A pdb=" N ARG A 290 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 311 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.591A pdb=" N VAL A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 Processing helix chain 'A' and resid 373 through 400 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.735A pdb=" N GLY B 120 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 121 " --> pdb=" O PRO B 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 121' Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.693A pdb=" N VAL B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.838A pdb=" N TYR B 354 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.654A pdb=" N ARG B 59 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 4 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLU B 165 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS B 6 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY B 167 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 8 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE B 169 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 10 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL B 171 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 211 removed outlier: 5.583A pdb=" N PHE B 361 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N CYS B 332 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS B 363 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 330 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 365 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 224 Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 322 through 324 362 hydrogen bonds defined for protein. 996 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: 0.92 Time building geometry restraints manager: 0.89 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: 1209 1.33 - 1.45: 1894 1.45 - 1.57: 3860 1.57 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 7008 Sorted by residual: bond pdb=" C17 MJC A 501 " pdb=" C18 MJC A 501 " ideal model delta sigma weight residual 1.337 1.572 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C12 MJC A 501 " pdb=" C13 MJC A 501 " ideal model delta sigma weight residual 1.334 1.539 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C7 MJC A 501 " pdb=" C8 MJC A 501 " ideal model delta sigma weight residual 1.336 1.540 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CG PRO A 128 " pdb=" CD PRO A 128 " ideal model delta sigma weight residual 1.503 1.379 0.124 3.40e-02 8.65e+02 1.33e+01 bond pdb=" C16 MJC A 501 " pdb=" C17 MJC A 501 " ideal model delta sigma weight residual 1.499 1.571 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 7003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 9465 3.11 - 6.22: 46 6.22 - 9.33: 6 9.33 - 12.44: 5 12.44 - 15.55: 7 Bond angle restraints: 9529 Sorted by residual: angle pdb=" N PRO A 128 " pdb=" CD PRO A 128 " pdb=" CG PRO A 128 " ideal model delta sigma weight residual 103.20 91.17 12.03 1.50e+00 4.44e-01 6.43e+01 angle pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" CD PRO A 128 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" C16 MJC A 501 " pdb=" C17 MJC A 501 " pdb=" C18 MJC A 501 " ideal model delta sigma weight residual 127.74 112.19 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C12 MJC A 501 " pdb=" C13 MJC A 501 " pdb=" C15 MJC A 501 " ideal model delta sigma weight residual 123.01 108.87 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C11 MJC A 501 " pdb=" C12 MJC A 501 " pdb=" C13 MJC A 501 " ideal model delta sigma weight residual 126.66 112.55 14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 9524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.24: 4004 30.24 - 60.48: 232 60.48 - 90.72: 7 90.72 - 120.96: 0 120.96 - 151.20: 1 Dihedral angle restraints: 4244 sinusoidal: 1833 harmonic: 2411 Sorted by residual: dihedral pdb=" C15 MJC A 501 " pdb=" C16 MJC A 501 " pdb=" C17 MJC A 501 " pdb=" C18 MJC A 501 " ideal model delta sinusoidal sigma weight residual 252.07 100.87 151.20 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CB CYS B 132 " pdb=" SG CYS B 132 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 127.15 -34.15 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA ASP B 135 " pdb=" CB ASP B 135 " pdb=" CG ASP B 135 " pdb=" OD1 ASP B 135 " ideal model delta sinusoidal sigma weight residual -30.00 -86.03 56.03 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 1077 1.059 - 2.118: 0 2.118 - 3.177: 0 3.177 - 4.236: 0 4.236 - 5.296: 1 Chirality restraints: 1078 Sorted by residual: chirality pdb=" C3 MJC A 501 " pdb=" C2 MJC A 501 " pdb=" C4 MJC A 501 " pdb=" C5 MJC A 501 " both_signs ideal model delta sigma weight residual False 2.58 -2.72 5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 35 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 319 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 1075 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 MJC A 501 " -0.431 2.00e-02 2.50e+03 4.92e-01 3.03e+03 pdb=" C6 MJC A 501 " -0.554 2.00e-02 2.50e+03 pdb=" C7 MJC A 501 " 0.688 2.00e-02 2.50e+03 pdb=" C8 MJC A 501 " 0.466 2.00e-02 2.50e+03 pdb=" C9 MJC A 501 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 MJC A 501 " 0.280 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C12 MJC A 501 " -0.573 2.00e-02 2.50e+03 pdb=" C13 MJC A 501 " 0.298 2.00e-02 2.50e+03 pdb=" C14 MJC A 501 " -0.011 2.00e-02 2.50e+03 pdb=" C15 MJC A 501 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 MJC A 501 " -0.180 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C17 MJC A 501 " 0.366 2.00e-02 2.50e+03 pdb=" C18 MJC A 501 " -0.305 2.00e-02 2.50e+03 pdb=" C19 MJC A 501 " 0.144 2.00e-02 2.50e+03 pdb=" C20 MJC A 501 " -0.025 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 713 2.75 - 3.29: 6558 3.29 - 3.82: 11065 3.82 - 4.36: 12351 4.36 - 4.90: 22178 Nonbonded interactions: 52865 Sorted by model distance: nonbonded pdb=" O LEU B 229 " pdb=" OG SER B 308 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" OD2 ASP A 395 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU A 140 " pdb=" O6' MJC A 501 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 260 " pdb=" OH TYR B 281 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" NZ LYS A 173 " model vdw 2.310 3.120 ... (remaining 52860 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 'C' selection = chain 'D' } 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: 0.750 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: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.235 7015 Z= 0.290 Angle : 0.772 15.548 9548 Z= 0.358 Chirality : 0.167 5.296 1078 Planarity : 0.019 0.492 1172 Dihedral : 16.883 151.198 2686 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 26.15 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.31), residues: 810 helix: 1.90 (0.29), residues: 339 sheet: 1.21 (0.39), residues: 188 loop : -0.95 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 63 TYR 0.016 0.001 TYR A 241 PHE 0.023 0.001 PHE A 150 TRP 0.011 0.001 TRP B 127 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 7008) covalent geometry : angle 0.76104 ( 9529) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.27952 ( 4) hydrogen bonds : bond 0.11789 ( 362) hydrogen bonds : angle 5.57729 ( 996) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 2.53841 ( 6) link_NAG-ASN : bond 0.00734 ( 3) link_NAG-ASN : angle 3.93914 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.339 Fit side-chains REVERT: A 120 MET cc_start: 0.8320 (mmm) cc_final: 0.8080 (mmm) REVERT: A 193 ASN cc_start: 0.8679 (m-40) cc_final: 0.8337 (m-40) REVERT: A 229 ASP cc_start: 0.8472 (t0) cc_final: 0.8163 (t0) REVERT: A 266 SER cc_start: 0.8004 (m) cc_final: 0.7780 (t) REVERT: A 277 MET cc_start: 0.8408 (mmm) cc_final: 0.8078 (mmp) REVERT: A 344 MET cc_start: 0.8089 (mtp) cc_final: 0.7865 (mtm) REVERT: B 333 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8549 (mm-40) REVERT: B 394 LEU cc_start: 0.8905 (tp) cc_final: 0.8680 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0616 time to fit residues: 9.8716 Evaluate side-chains 94 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097127 restraints weight = 10683.233| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.81 r_work: 0.2969 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7015 Z= 0.109 Angle : 0.548 9.649 9548 Z= 0.271 Chirality : 0.044 0.338 1078 Planarity : 0.004 0.040 1172 Dihedral : 9.870 142.017 1114 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.29 % Allowed : 24.53 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.31), residues: 810 helix: 2.48 (0.28), residues: 333 sheet: 1.18 (0.40), residues: 170 loop : -0.69 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.015 0.001 TYR A 241 PHE 0.025 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7008) covalent geometry : angle 0.53547 ( 9529) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.21082 ( 4) hydrogen bonds : bond 0.03558 ( 362) hydrogen bonds : angle 4.40448 ( 996) link_BETA1-4 : bond 0.00435 ( 2) link_BETA1-4 : angle 2.57415 ( 6) link_NAG-ASN : bond 0.00827 ( 3) link_NAG-ASN : angle 3.24582 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.269 Fit side-chains REVERT: A 229 ASP cc_start: 0.8550 (t0) cc_final: 0.8269 (t0) REVERT: A 266 SER cc_start: 0.7649 (m) cc_final: 0.7430 (t) REVERT: A 268 LEU cc_start: 0.8575 (tt) cc_final: 0.8371 (tt) REVERT: B 98 TYR cc_start: 0.8866 (m-80) cc_final: 0.8390 (m-80) REVERT: B 333 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8593 (mm-40) outliers start: 17 outliers final: 8 residues processed: 115 average time/residue: 0.0624 time to fit residues: 10.7391 Evaluate side-chains 100 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 293 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096918 restraints weight = 10534.386| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.80 r_work: 0.2966 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7015 Z= 0.121 Angle : 0.536 9.545 9548 Z= 0.268 Chirality : 0.044 0.328 1078 Planarity : 0.003 0.039 1172 Dihedral : 9.594 134.661 1114 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 23.58 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.31), residues: 810 helix: 2.54 (0.28), residues: 336 sheet: 1.19 (0.40), residues: 170 loop : -0.70 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 405 TYR 0.016 0.001 TYR A 57 PHE 0.022 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7008) covalent geometry : angle 0.52319 ( 9529) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.18258 ( 4) hydrogen bonds : bond 0.03525 ( 362) hydrogen bonds : angle 4.29884 ( 996) link_BETA1-4 : bond 0.00441 ( 2) link_BETA1-4 : angle 2.65423 ( 6) link_NAG-ASN : bond 0.00788 ( 3) link_NAG-ASN : angle 3.19803 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6460 (m-80) cc_final: 0.6234 (m-80) REVERT: A 191 HIS cc_start: 0.9034 (OUTLIER) cc_final: 0.8312 (t-90) REVERT: A 229 ASP cc_start: 0.8573 (t0) cc_final: 0.8251 (t0) REVERT: A 266 SER cc_start: 0.7660 (m) cc_final: 0.7421 (t) REVERT: B 40 ASP cc_start: 0.8513 (m-30) cc_final: 0.7964 (t70) REVERT: B 98 TYR cc_start: 0.8888 (m-80) cc_final: 0.8422 (m-80) REVERT: B 204 PHE cc_start: 0.8210 (t80) cc_final: 0.7974 (t80) REVERT: B 333 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8525 (mm-40) REVERT: B 399 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8793 (mp) outliers start: 22 outliers final: 13 residues processed: 112 average time/residue: 0.0601 time to fit residues: 10.1411 Evaluate side-chains 107 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094504 restraints weight = 10755.955| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.83 r_work: 0.2919 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7015 Z= 0.169 Angle : 0.579 9.628 9548 Z= 0.289 Chirality : 0.045 0.327 1078 Planarity : 0.004 0.040 1172 Dihedral : 9.446 129.773 1114 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.50 % Allowed : 23.32 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 810 helix: 2.68 (0.28), residues: 331 sheet: 1.01 (0.39), residues: 172 loop : -0.73 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.016 0.002 TYR A 57 PHE 0.021 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7008) covalent geometry : angle 0.56703 ( 9529) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.32723 ( 4) hydrogen bonds : bond 0.03886 ( 362) hydrogen bonds : angle 4.29519 ( 996) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 2.71610 ( 6) link_NAG-ASN : bond 0.00788 ( 3) link_NAG-ASN : angle 3.17843 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6477 (m-80) cc_final: 0.6266 (m-80) REVERT: A 191 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8536 (t-90) REVERT: A 229 ASP cc_start: 0.8494 (t0) cc_final: 0.8223 (t0) REVERT: A 266 SER cc_start: 0.7794 (m) cc_final: 0.7553 (t) REVERT: A 394 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 401 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 40 ASP cc_start: 0.8538 (m-30) cc_final: 0.7977 (t70) REVERT: B 98 TYR cc_start: 0.8900 (m-80) cc_final: 0.8409 (m-80) REVERT: B 399 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (mp) outliers start: 26 outliers final: 17 residues processed: 106 average time/residue: 0.0601 time to fit residues: 9.6403 Evaluate side-chains 108 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097351 restraints weight = 10600.247| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.81 r_work: 0.2970 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7015 Z= 0.105 Angle : 0.530 9.527 9548 Z= 0.266 Chirality : 0.044 0.325 1078 Planarity : 0.003 0.039 1172 Dihedral : 9.184 131.816 1114 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.10 % Allowed : 23.85 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 810 helix: 2.77 (0.28), residues: 331 sheet: 1.27 (0.38), residues: 180 loop : -0.75 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.015 0.001 TYR A 57 PHE 0.021 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7008) covalent geometry : angle 0.51851 ( 9529) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.21930 ( 4) hydrogen bonds : bond 0.03304 ( 362) hydrogen bonds : angle 4.19158 ( 996) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 2.35662 ( 6) link_NAG-ASN : bond 0.00812 ( 3) link_NAG-ASN : angle 3.14440 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6481 (m-80) cc_final: 0.6279 (m-80) REVERT: A 119 ILE cc_start: 0.8540 (mp) cc_final: 0.7964 (tt) REVERT: A 191 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8502 (t-90) REVERT: A 229 ASP cc_start: 0.8417 (t0) cc_final: 0.8141 (t0) REVERT: A 266 SER cc_start: 0.7723 (m) cc_final: 0.7516 (t) REVERT: A 365 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: B 40 ASP cc_start: 0.8523 (m-30) cc_final: 0.7997 (t70) REVERT: B 98 TYR cc_start: 0.8896 (m-80) cc_final: 0.8412 (m-80) REVERT: B 399 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8860 (mp) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.0580 time to fit residues: 9.6850 Evaluate side-chains 111 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095778 restraints weight = 10763.670| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.82 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7015 Z= 0.143 Angle : 0.562 9.540 9548 Z= 0.279 Chirality : 0.044 0.326 1078 Planarity : 0.003 0.040 1172 Dihedral : 9.144 125.987 1114 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.91 % Allowed : 23.45 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 810 helix: 2.76 (0.28), residues: 330 sheet: 1.11 (0.38), residues: 184 loop : -0.72 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.016 0.001 TYR A 57 PHE 0.020 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7008) covalent geometry : angle 0.55033 ( 9529) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.28142 ( 4) hydrogen bonds : bond 0.03616 ( 362) hydrogen bonds : angle 4.22797 ( 996) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 2.42676 ( 6) link_NAG-ASN : bond 0.00799 ( 3) link_NAG-ASN : angle 3.15916 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8586 (mp) cc_final: 0.8076 (tt) REVERT: A 191 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8596 (t-90) REVERT: A 229 ASP cc_start: 0.8409 (t0) cc_final: 0.8154 (t0) REVERT: A 266 SER cc_start: 0.7733 (m) cc_final: 0.7507 (t) REVERT: A 289 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.6845 (mmt180) REVERT: A 365 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: A 398 ILE cc_start: 0.9142 (mm) cc_final: 0.8937 (mm) REVERT: B 40 ASP cc_start: 0.8522 (m-30) cc_final: 0.7978 (t70) REVERT: B 98 TYR cc_start: 0.8922 (m-80) cc_final: 0.8422 (m-80) REVERT: B 188 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7615 (m-90) REVERT: B 399 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8856 (mp) outliers start: 29 outliers final: 20 residues processed: 115 average time/residue: 0.0633 time to fit residues: 10.7906 Evaluate side-chains 117 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 188 TRP Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097048 restraints weight = 10585.897| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.81 r_work: 0.2961 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7015 Z= 0.114 Angle : 0.539 9.552 9548 Z= 0.267 Chirality : 0.044 0.325 1078 Planarity : 0.003 0.039 1172 Dihedral : 9.023 124.527 1114 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.37 % Allowed : 23.99 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.30), residues: 810 helix: 2.80 (0.28), residues: 330 sheet: 1.38 (0.39), residues: 180 loop : -0.74 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.016 0.001 TYR A 57 PHE 0.020 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7008) covalent geometry : angle 0.52759 ( 9529) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.23122 ( 4) hydrogen bonds : bond 0.03376 ( 362) hydrogen bonds : angle 4.17310 ( 996) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 2.20285 ( 6) link_NAG-ASN : bond 0.00800 ( 3) link_NAG-ASN : angle 3.15321 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8597 (mp) cc_final: 0.8097 (tt) REVERT: A 191 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8541 (t-90) REVERT: A 229 ASP cc_start: 0.8327 (t0) cc_final: 0.8075 (t0) REVERT: A 266 SER cc_start: 0.7730 (m) cc_final: 0.7516 (t) REVERT: A 277 MET cc_start: 0.8261 (mmm) cc_final: 0.8026 (mmp) REVERT: A 289 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.6838 (mmt180) REVERT: A 365 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: B 40 ASP cc_start: 0.8513 (m-30) cc_final: 0.7995 (t70) REVERT: B 98 TYR cc_start: 0.8910 (m-80) cc_final: 0.8412 (m-80) REVERT: B 399 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8868 (mp) outliers start: 25 outliers final: 19 residues processed: 114 average time/residue: 0.0647 time to fit residues: 10.4356 Evaluate side-chains 115 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094414 restraints weight = 10791.330| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.79 r_work: 0.2923 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7015 Z= 0.173 Angle : 0.590 10.100 9548 Z= 0.293 Chirality : 0.045 0.325 1078 Planarity : 0.004 0.040 1172 Dihedral : 9.171 125.753 1114 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.37 % Allowed : 23.85 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.30), residues: 810 helix: 2.75 (0.28), residues: 330 sheet: 1.28 (0.39), residues: 170 loop : -0.79 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 59 TYR 0.018 0.002 TYR A 57 PHE 0.021 0.001 PHE A 150 TRP 0.009 0.001 TRP B 110 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7008) covalent geometry : angle 0.57993 ( 9529) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.39119 ( 4) hydrogen bonds : bond 0.03923 ( 362) hydrogen bonds : angle 4.27137 ( 996) link_BETA1-4 : bond 0.00327 ( 2) link_BETA1-4 : angle 2.32974 ( 6) link_NAG-ASN : bond 0.00809 ( 3) link_NAG-ASN : angle 3.18381 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8585 (mp) cc_final: 0.8152 (tt) REVERT: A 191 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8695 (t-90) REVERT: A 229 ASP cc_start: 0.8459 (t0) cc_final: 0.8185 (t0) REVERT: A 266 SER cc_start: 0.7823 (m) cc_final: 0.7608 (t) REVERT: A 289 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.6827 (mmt180) REVERT: A 365 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: B 40 ASP cc_start: 0.8521 (m-30) cc_final: 0.8056 (t0) REVERT: B 399 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8855 (mp) outliers start: 25 outliers final: 20 residues processed: 111 average time/residue: 0.0613 time to fit residues: 10.0195 Evaluate side-chains 114 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096677 restraints weight = 10745.840| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.83 r_work: 0.2963 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7015 Z= 0.114 Angle : 0.559 10.852 9548 Z= 0.277 Chirality : 0.044 0.324 1078 Planarity : 0.003 0.040 1172 Dihedral : 8.951 122.726 1114 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.10 % Allowed : 23.85 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.30), residues: 810 helix: 2.69 (0.28), residues: 335 sheet: 1.25 (0.39), residues: 183 loop : -0.69 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 63 TYR 0.016 0.001 TYR A 57 PHE 0.020 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7008) covalent geometry : angle 0.54914 ( 9529) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.24125 ( 4) hydrogen bonds : bond 0.03392 ( 362) hydrogen bonds : angle 4.17544 ( 996) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 2.06326 ( 6) link_NAG-ASN : bond 0.00789 ( 3) link_NAG-ASN : angle 3.14921 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8573 (mp) cc_final: 0.8123 (tt) REVERT: A 191 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8569 (t-90) REVERT: A 229 ASP cc_start: 0.8302 (t0) cc_final: 0.8049 (t0) REVERT: A 266 SER cc_start: 0.7785 (m) cc_final: 0.7569 (t) REVERT: A 289 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.6812 (mmt180) REVERT: A 365 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: A 398 ILE cc_start: 0.9068 (mm) cc_final: 0.8843 (mm) REVERT: B 40 ASP cc_start: 0.8510 (m-30) cc_final: 0.7976 (t70) REVERT: B 399 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8857 (mp) outliers start: 23 outliers final: 18 residues processed: 113 average time/residue: 0.0662 time to fit residues: 10.9547 Evaluate side-chains 113 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097489 restraints weight = 10657.595| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.84 r_work: 0.2969 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7015 Z= 0.106 Angle : 0.550 11.469 9548 Z= 0.273 Chirality : 0.043 0.323 1078 Planarity : 0.003 0.040 1172 Dihedral : 8.729 120.339 1114 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.70 % Allowed : 23.99 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.30), residues: 810 helix: 2.70 (0.28), residues: 336 sheet: 1.51 (0.39), residues: 176 loop : -0.64 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 340 TYR 0.015 0.001 TYR A 241 PHE 0.019 0.001 PHE A 210 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7008) covalent geometry : angle 0.54013 ( 9529) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.22231 ( 4) hydrogen bonds : bond 0.03215 ( 362) hydrogen bonds : angle 4.13715 ( 996) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 1.95809 ( 6) link_NAG-ASN : bond 0.00799 ( 3) link_NAG-ASN : angle 3.15098 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8577 (mp) cc_final: 0.8161 (tt) REVERT: A 191 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8563 (t-90) REVERT: A 229 ASP cc_start: 0.8331 (t0) cc_final: 0.8103 (t0) REVERT: A 266 SER cc_start: 0.7785 (m) cc_final: 0.7528 (t) REVERT: A 277 MET cc_start: 0.8245 (mmm) cc_final: 0.7974 (mmp) REVERT: A 289 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.6822 (mmt180) REVERT: A 365 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: A 398 ILE cc_start: 0.9046 (mm) cc_final: 0.8836 (mm) REVERT: B 40 ASP cc_start: 0.8512 (m-30) cc_final: 0.7944 (t70) REVERT: B 333 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8503 (mm-40) REVERT: B 399 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8860 (mp) outliers start: 20 outliers final: 16 residues processed: 115 average time/residue: 0.0675 time to fit residues: 11.2120 Evaluate side-chains 110 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 46 optimal weight: 0.2980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097118 restraints weight = 10698.861| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.82 r_work: 0.2966 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7015 Z= 0.120 Angle : 0.567 11.036 9548 Z= 0.280 Chirality : 0.044 0.323 1078 Planarity : 0.003 0.039 1172 Dihedral : 8.697 119.545 1114 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.70 % Allowed : 24.39 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.30), residues: 810 helix: 2.73 (0.28), residues: 336 sheet: 1.55 (0.39), residues: 176 loop : -0.63 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 59 TYR 0.015 0.001 TYR A 241 PHE 0.021 0.001 PHE A 150 TRP 0.009 0.001 TRP A 355 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7008) covalent geometry : angle 0.55703 ( 9529) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.24654 ( 4) hydrogen bonds : bond 0.03282 ( 362) hydrogen bonds : angle 4.13864 ( 996) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 1.95379 ( 6) link_NAG-ASN : bond 0.00790 ( 3) link_NAG-ASN : angle 3.15531 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.93 seconds wall clock time: 25 minutes 39.54 seconds (1539.54 seconds total)