Starting phenix.real_space_refine on Thu Oct 22 20:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.map" model { file = "/net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nx_67855/10_2026/21nx_67855.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3070 2.51 5 N 822 2.21 5 O 948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1380 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 162} Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1669 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 194} Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1699 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: 1.10, per 1000 atoms: 0.23 Number of scatterers: 4860 At special positions: 0 Unit cell: (65.55, 83.6, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 948 8.00 N 822 7.00 C 3070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 4 " NAG-ASN " NAG A 301 " - " ASN A 62 " " NAG D 1 " - " ASN B 297 " " NAG E 1 " - " ASN C 297 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 180.0 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 7.4% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 413 through 420 removed outlier: 3.632A pdb=" N GLU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 414 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.598A pdb=" N ASP A 30 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 43 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 42 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.603A pdb=" N LYS A 58 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.557A pdb=" N TYR A 140 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 149 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 138 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS A 151 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 136 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS A 137 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 174 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 180 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.557A pdb=" N TYR A 140 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 149 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 138 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS A 151 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 136 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS A 137 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 174 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 243 removed outlier: 4.186A pdb=" N ASP B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 300 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.744A pdb=" N ARG B 334 " --> pdb=" O CYS B 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 351 Processing sheet with id=AA9, first strand: chain 'B' and resid 347 through 351 Processing sheet with id=AB1, first strand: chain 'B' and resid 386 through 387 removed outlier: 3.571A pdb=" N PHE B 423 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.572A pdb=" N SER C 239 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR C 260 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 304 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 305 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 274 through 279 Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.590A pdb=" N GLN C 347 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET C 412 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 365 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.590A pdb=" N GLN C 347 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET C 412 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 365 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 386 through 388 removed outlier: 4.714A pdb=" N TRP C 381 " --> pdb=" O GLU C 388 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 465 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: 0.55 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 797 1.29 - 1.42: 1270 1.42 - 1.55: 2881 1.55 - 1.68: 1 1.68 - 1.81: 28 Bond restraints: 4977 Sorted by residual: bond pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 1.522 1.434 0.088 1.35e-02 5.49e+03 4.27e+01 bond pdb=" C PHE A 150 " pdb=" O PHE A 150 " ideal model delta sigma weight residual 1.235 1.162 0.074 1.19e-02 7.06e+03 3.85e+01 bond pdb=" CA PHE A 150 " pdb=" CB PHE A 150 " ideal model delta sigma weight residual 1.527 1.455 0.073 1.30e-02 5.92e+03 3.13e+01 bond pdb=" C LYS A 148 " pdb=" O LYS A 148 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.29e-02 6.01e+03 2.90e+01 bond pdb=" CA VAL B 266 " pdb=" C VAL B 266 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.16e-02 7.43e+03 2.89e+01 ... (remaining 4972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 6571 2.10 - 4.20: 148 4.20 - 6.30: 37 6.30 - 8.39: 7 8.39 - 10.49: 3 Bond angle restraints: 6766 Sorted by residual: angle pdb=" N PRO C 232 " pdb=" CA PRO C 232 " pdb=" C PRO C 232 " ideal model delta sigma weight residual 114.68 105.70 8.98 1.28e+00 6.10e-01 4.92e+01 angle pdb=" N LEU C 234 " pdb=" CA LEU C 234 " pdb=" C LEU C 234 " ideal model delta sigma weight residual 109.62 99.13 10.49 1.50e+00 4.44e-01 4.89e+01 angle pdb=" C ALA C 231 " pdb=" N PRO C 232 " pdb=" CA PRO C 232 " ideal model delta sigma weight residual 120.94 114.92 6.02 1.14e+00 7.69e-01 2.79e+01 angle pdb=" N VAL B 266 " pdb=" CA VAL B 266 " pdb=" C VAL B 266 " ideal model delta sigma weight residual 109.17 101.40 7.77 1.54e+00 4.22e-01 2.55e+01 angle pdb=" N PHE A 150 " pdb=" CA PHE A 150 " pdb=" CB PHE A 150 " ideal model delta sigma weight residual 110.37 102.12 8.25 1.65e+00 3.67e-01 2.50e+01 ... (remaining 6761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 2933 21.97 - 43.95: 161 43.95 - 65.92: 20 65.92 - 87.90: 14 87.90 - 109.87: 8 Dihedral angle restraints: 3136 sinusoidal: 1393 harmonic: 1743 Sorted by residual: dihedral pdb=" CA ARG B 344 " pdb=" C ARG B 344 " pdb=" N ALA B 345 " pdb=" CA ALA B 345 " ideal model delta harmonic sigma weight residual 180.00 141.39 38.61 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" N PHE A 150 " pdb=" C PHE A 150 " pdb=" CA PHE A 150 " pdb=" CB PHE A 150 " ideal model delta harmonic sigma weight residual 122.80 111.21 11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" CA LYS B 413 " pdb=" C LYS B 413 " pdb=" N THR B 414 " pdb=" CA THR B 414 " ideal model delta harmonic sigma weight residual 180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 612 0.052 - 0.104: 117 0.104 - 0.156: 43 0.156 - 0.209: 8 0.209 - 0.261: 2 Chirality restraints: 782 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.78e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 779 not shown) Planarity restraints: 857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 265 " -0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ASP B 265 " 0.082 2.00e-02 2.50e+03 pdb=" O ASP B 265 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL B 266 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 237 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 238 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 146 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C GLY A 146 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 146 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 147 " -0.010 2.00e-02 2.50e+03 ... (remaining 854 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 186 2.71 - 3.25: 4401 3.25 - 3.80: 7182 3.80 - 4.35: 9388 4.35 - 4.90: 16402 Nonbonded interactions: 37559 Sorted by model distance: nonbonded pdb=" NZ LYS A 114 " pdb=" O LEU A 116 " model vdw 2.158 3.120 nonbonded pdb=" NZ LYS B 413 " pdb=" OG SER B 415 " model vdw 2.188 3.120 nonbonded pdb=" ND2 ASN B 390 " pdb=" O ASN B 411 " model vdw 2.211 3.120 nonbonded pdb=" O HIS A 61 " pdb=" OG SER A 64 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP A 40 " pdb=" NE2 HIS A 128 " model vdw 2.251 3.120 ... (remaining 37554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 236 through 444) selection = (chain 'C' and resid 236 through 444) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.660 Find NCS groups from input model: 0.060 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:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 0.088 4992 Z= 0.424 Angle : 0.821 10.492 6805 Z= 0.446 Chirality : 0.051 0.261 782 Planarity : 0.005 0.071 854 Dihedral : 15.620 109.871 1986 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.73 % Allowed : 2.36 % Favored : 96.91 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.34 (0.38), residues: 589 helix: -2.49 (0.77), residues: 40 sheet: -0.40 (0.35), residues: 267 loop : -1.02 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 360 TYR 0.007 0.001 TYR C 407 PHE 0.020 0.002 PHE A 150 TRP 0.007 0.001 TRP B 381 HIS 0.004 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.42 ( 4977) covalent geometry : angle 0.80518 / 0.44 ( 6766) SS BOND : bond 0.00276 / 0.19 ( 6) SS BOND : angle 0.57677 / 0.33 ( 12) hydrogen bonds : bond 0.26889 / 18.07 ( 153) hydrogen bonds : angle 9.25852 / 6.30 ( 465) link_BETA1-4 : bond 0.00646 / 0.41 ( 4) link_BETA1-4 : angle 3.19378 / 1.60 ( 12) link_BETA1-6 : bond 0.01714 / 0.95 ( 2) link_BETA1-6 : angle 2.19204 / 1.27 ( 6) link_NAG-ASN : bond 0.00306 / 0.16 ( 3) link_NAG-ASN : angle 2.09647 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7928 (tptt) cc_final: 0.7541 (ttmt) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.5404 time to fit residues: 41.6486 Evaluate side-chains 64 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 328 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 58] chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN B 310 HIS B 325 ASN B 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153985 restraints weight = 5330.559| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.18 r_work: 0.3670 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4992 Z= 0.158 Angle : 0.668 6.622 6805 Z= 0.339 Chirality : 0.048 0.196 782 Planarity : 0.005 0.069 854 Dihedral : 10.939 71.032 816 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.36 % Allowed : 10.34 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.18 (0.37), residues: 589 helix: -1.82 (0.83), residues: 42 sheet: -0.34 (0.34), residues: 271 loop : -0.97 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.012 0.002 TYR A 169 PHE 0.014 0.002 PHE A 170 TRP 0.009 0.001 TRP B 277 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4977) covalent geometry : angle 0.65213 / 0.34 ( 6766) SS BOND : bond 0.00443 / 0.32 ( 6) SS BOND : angle 0.63665 / 0.39 ( 12) hydrogen bonds : bond 0.04483 / 2.90 ( 153) hydrogen bonds : angle 6.34159 / 4.54 ( 465) link_BETA1-4 : bond 0.00276 / 0.18 ( 4) link_BETA1-4 : angle 3.01885 / 1.51 ( 12) link_BETA1-6 : bond 0.00228 / 0.13 ( 2) link_BETA1-6 : angle 1.66284 / 0.98 ( 6) link_NAG-ASN : bond 0.00100 / 0.06 ( 3) link_NAG-ASN : angle 1.86012 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7802 (tptt) cc_final: 0.7404 (ttmt) REVERT: B 380 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 412 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6445 (ptm) outliers start: 13 outliers final: 4 residues processed: 63 average time/residue: 0.5833 time to fit residues: 38.2093 Evaluate side-chains 60 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 412 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [10, 37, 54, 11, 42, 31, 7, 30, 15, 27, 53] chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 53 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN B 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145102 restraints weight = 5271.622| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.43 r_work: 0.3591 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4992 Z= 0.128 Angle : 0.623 7.073 6805 Z= 0.314 Chirality : 0.046 0.188 782 Planarity : 0.004 0.069 854 Dihedral : 8.851 55.825 813 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.54 % Allowed : 13.43 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.08 (0.36), residues: 589 helix: -1.48 (0.85), residues: 41 sheet: -0.30 (0.34), residues: 269 loop : -0.92 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 360 TYR 0.010 0.001 TYR A 169 PHE 0.013 0.001 PHE A 170 TRP 0.008 0.001 TRP B 277 HIS 0.007 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4977) covalent geometry : angle 0.60683 / 0.31 ( 6766) SS BOND : bond 0.00338 / 0.24 ( 6) SS BOND : angle 0.42827 / 0.27 ( 12) hydrogen bonds : bond 0.03840 / 2.48 ( 153) hydrogen bonds : angle 5.69074 / 4.08 ( 465) link_BETA1-4 : bond 0.00217 / 0.15 ( 4) link_BETA1-4 : angle 2.89135 / 1.46 ( 12) link_BETA1-6 : bond 0.00151 / 0.08 ( 2) link_BETA1-6 : angle 1.47280 / 0.88 ( 6) link_NAG-ASN : bond 0.00109 / 0.06 ( 3) link_NAG-ASN : angle 1.82352 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.192 Fit side-chains REVERT: A 148 LYS cc_start: 0.7775 (tptt) cc_final: 0.7200 (ttmt) REVERT: B 412 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6251 (ptm) REVERT: B 413 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5872 (mttp) outliers start: 14 outliers final: 3 residues processed: 58 average time/residue: 0.5569 time to fit residues: 33.7075 Evaluate side-chains 52 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [17, 50, 53, 5, 13, 57, 52, 39, 44, 54, 30] chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 52 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS B 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.179691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147218 restraints weight = 5264.199| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.27 r_work: 0.3637 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4992 Z= 0.108 Angle : 0.573 6.724 6805 Z= 0.288 Chirality : 0.046 0.170 782 Planarity : 0.004 0.070 854 Dihedral : 6.421 38.120 813 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 15.06 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.92 (0.36), residues: 589 helix: -1.37 (0.85), residues: 41 sheet: -0.22 (0.33), residues: 271 loop : -0.77 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.008 0.001 TYR C 407 PHE 0.012 0.001 PHE A 170 TRP 0.006 0.001 TRP B 277 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4977) covalent geometry : angle 0.55767 / 0.29 ( 6766) SS BOND : bond 0.00282 / 0.20 ( 6) SS BOND : angle 0.43474 / 0.28 ( 12) hydrogen bonds : bond 0.03268 / 2.10 ( 153) hydrogen bonds : angle 5.15962 / 3.74 ( 465) link_BETA1-4 : bond 0.00259 / 0.17 ( 4) link_BETA1-4 : angle 2.69488 / 1.35 ( 12) link_BETA1-6 : bond 0.00128 / 0.08 ( 2) link_BETA1-6 : angle 1.36080 / 0.82 ( 6) link_NAG-ASN : bond 0.00125 / 0.07 ( 3) link_NAG-ASN : angle 1.68952 / 0.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.187 Fit side-chains REVERT: A 148 LYS cc_start: 0.7878 (tptt) cc_final: 0.7327 (ttmt) REVERT: B 295 ASP cc_start: 0.7180 (m-30) cc_final: 0.6876 (m-30) REVERT: B 412 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6076 (ptm) REVERT: B 413 LYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5623 (mtpp) REVERT: C 428 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7474 (mtt180) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 0.4616 time to fit residues: 28.6599 Evaluate side-chains 55 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [2, 26, 1, 32, 20, 13, 35, 42, 8, 25, 52] chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN B 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141907 restraints weight = 5396.828| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.44 r_work: 0.3588 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4992 Z= 0.152 Angle : 0.611 6.843 6805 Z= 0.308 Chirality : 0.047 0.175 782 Planarity : 0.004 0.072 854 Dihedral : 6.259 40.627 813 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.27 % Allowed : 14.52 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.35), residues: 589 helix: -1.99 (0.73), residues: 48 sheet: -0.00 (0.34), residues: 253 loop : -1.14 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.012 0.001 TYR C 407 PHE 0.018 0.002 PHE C 372 TRP 0.007 0.001 TRP C 417 HIS 0.008 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 4977) covalent geometry : angle 0.59532 / 0.30 ( 6766) SS BOND : bond 0.00357 / 0.25 ( 6) SS BOND : angle 0.47223 / 0.30 ( 12) hydrogen bonds : bond 0.03601 / 2.29 ( 153) hydrogen bonds : angle 5.08087 / 3.70 ( 465) link_BETA1-4 : bond 0.00272 / 0.18 ( 4) link_BETA1-4 : angle 2.87729 / 1.48 ( 12) link_BETA1-6 : bond 0.00160 / 0.09 ( 2) link_BETA1-6 : angle 1.58870 / 0.96 ( 6) link_NAG-ASN : bond 0.00156 / 0.09 ( 3) link_NAG-ASN : angle 1.64587 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.189 Fit side-chains REVERT: A 148 LYS cc_start: 0.7891 (tptt) cc_final: 0.7293 (ttmt) REVERT: B 295 ASP cc_start: 0.7066 (m-30) cc_final: 0.6778 (m-30) REVERT: B 336 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 380 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: B 412 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6252 (ptm) REVERT: B 413 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5751 (mtpp) outliers start: 18 outliers final: 7 residues processed: 62 average time/residue: 0.5126 time to fit residues: 33.2397 Evaluate side-chains 59 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [41, 8, 54, 32, 55, 51, 12, 17, 33, 26, 49] chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144890 restraints weight = 5372.208| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.44 r_work: 0.3589 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4992 Z= 0.140 Angle : 0.597 6.768 6805 Z= 0.303 Chirality : 0.046 0.203 782 Planarity : 0.004 0.073 854 Dihedral : 5.894 41.042 813 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.90 % Allowed : 15.25 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.04 (0.36), residues: 589 helix: -1.59 (0.81), residues: 42 sheet: -0.26 (0.33), residues: 267 loop : -0.86 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 428 TYR 0.012 0.001 TYR C 407 PHE 0.016 0.002 PHE C 372 TRP 0.006 0.001 TRP C 417 HIS 0.002 0.001 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4977) covalent geometry : angle 0.58286 / 0.30 ( 6766) SS BOND : bond 0.00306 / 0.21 ( 6) SS BOND : angle 0.48331 / 0.31 ( 12) hydrogen bonds : bond 0.03407 / 2.16 ( 153) hydrogen bonds : angle 4.97125 / 3.62 ( 465) link_BETA1-4 : bond 0.00250 / 0.16 ( 4) link_BETA1-4 : angle 2.67843 / 1.36 ( 12) link_BETA1-6 : bond 0.00101 / 0.06 ( 2) link_BETA1-6 : angle 1.53428 / 0.92 ( 6) link_NAG-ASN : bond 0.00128 / 0.07 ( 3) link_NAG-ASN : angle 1.64707 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7900 (tptt) cc_final: 0.7318 (ttmt) REVERT: B 295 ASP cc_start: 0.7066 (m-30) cc_final: 0.6775 (m-30) REVERT: B 336 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 380 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: B 412 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6170 (ptm) outliers start: 16 outliers final: 9 residues processed: 59 average time/residue: 0.5198 time to fit residues: 32.0521 Evaluate side-chains 59 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [11, 24, 38, 35, 56, 58, 23, 22, 32, 42, 48] chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 42 optimal weight: 0.0370 chunk 48 optimal weight: 0.9980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149261 restraints weight = 5254.155| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.40 r_work: 0.3615 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4992 Z= 0.101 Angle : 0.551 8.057 6805 Z= 0.281 Chirality : 0.045 0.182 782 Planarity : 0.004 0.073 854 Dihedral : 5.071 37.875 813 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.00 % Allowed : 16.88 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.82 (0.35), residues: 589 helix: -1.47 (0.81), residues: 42 sheet: 0.04 (0.34), residues: 255 loop : -0.87 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 428 TYR 0.007 0.001 TYR C 407 PHE 0.011 0.001 PHE A 170 TRP 0.007 0.001 TRP B 277 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 4977) covalent geometry : angle 0.53924 / 0.28 ( 6766) SS BOND : bond 0.00218 / 0.16 ( 6) SS BOND : angle 0.40293 / 0.26 ( 12) hydrogen bonds : bond 0.02984 / 1.93 ( 153) hydrogen bonds : angle 4.76195 / 3.48 ( 465) link_BETA1-4 : bond 0.00290 / 0.20 ( 4) link_BETA1-4 : angle 2.25006 / 1.13 ( 12) link_BETA1-6 : bond 0.00194 / 0.12 ( 2) link_BETA1-6 : angle 1.26991 / 0.77 ( 6) link_NAG-ASN : bond 0.00146 / 0.08 ( 3) link_NAG-ASN : angle 1.60354 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.187 Fit side-chains REVERT: A 148 LYS cc_start: 0.7899 (tptt) cc_final: 0.7294 (ttmt) REVERT: B 380 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: B 413 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5611 (mtpp) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.4275 time to fit residues: 23.6096 Evaluate side-chains 51 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [36, 13, 16, 31, 1, 10, 51, 4, 32, 40, 43] chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146840 restraints weight = 5327.775| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.41 r_work: 0.3613 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4992 Z= 0.124 Angle : 0.569 6.595 6805 Z= 0.289 Chirality : 0.045 0.182 782 Planarity : 0.004 0.073 854 Dihedral : 5.152 39.472 811 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.54 % Allowed : 17.24 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.35), residues: 589 helix: -1.50 (0.81), residues: 42 sheet: -0.11 (0.33), residues: 262 loop : -0.73 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.010 0.001 TYR C 407 PHE 0.016 0.002 PHE C 372 TRP 0.007 0.001 TRP C 417 HIS 0.002 0.001 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 4977) covalent geometry : angle 0.55635 / 0.29 ( 6766) SS BOND : bond 0.00273 / 0.19 ( 6) SS BOND : angle 0.42876 / 0.27 ( 12) hydrogen bonds : bond 0.03201 / 2.05 ( 153) hydrogen bonds : angle 4.72651 / 3.45 ( 465) link_BETA1-4 : bond 0.00236 / 0.16 ( 4) link_BETA1-4 : angle 2.43494 / 1.27 ( 12) link_BETA1-6 : bond 0.00022 / 0.01 ( 2) link_BETA1-6 : angle 1.47271 / 0.89 ( 6) link_NAG-ASN : bond 0.00119 / 0.06 ( 3) link_NAG-ASN : angle 1.45521 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.159 Fit side-chains REVERT: A 148 LYS cc_start: 0.7897 (tptt) cc_final: 0.7300 (ttmt) REVERT: B 380 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6939 (mt-10) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.4734 time to fit residues: 25.9020 Evaluate side-chains 51 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [17, 49, 19, 54, 51, 23, 56, 15, 35, 58, 9] chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141876 restraints weight = 5346.228| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.43 r_work: 0.3591 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4992 Z= 0.145 Angle : 0.593 6.797 6805 Z= 0.301 Chirality : 0.046 0.187 782 Planarity : 0.004 0.074 854 Dihedral : 5.520 41.122 811 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.36 % Allowed : 17.79 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.92 (0.35), residues: 589 helix: -1.58 (0.81), residues: 42 sheet: -0.14 (0.33), residues: 260 loop : -0.81 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.012 0.001 TYR C 407 PHE 0.018 0.002 PHE C 372 TRP 0.008 0.001 TRP C 417 HIS 0.004 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4977) covalent geometry : angle 0.58052 / 0.30 ( 6766) SS BOND : bond 0.00312 / 0.22 ( 6) SS BOND : angle 0.47044 / 0.30 ( 12) hydrogen bonds : bond 0.03468 / 2.18 ( 153) hydrogen bonds : angle 4.78070 / 3.48 ( 465) link_BETA1-4 : bond 0.00245 / 0.16 ( 4) link_BETA1-4 : angle 2.55706 / 1.33 ( 12) link_BETA1-6 : bond 0.00121 / 0.07 ( 2) link_BETA1-6 : angle 1.57765 / 0.95 ( 6) link_NAG-ASN : bond 0.00127 / 0.07 ( 3) link_NAG-ASN : angle 1.48426 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.161 Fit side-chains REVERT: A 79 ARG cc_start: 0.6155 (mmt180) cc_final: 0.5912 (mmt180) REVERT: A 148 LYS cc_start: 0.7968 (tptt) cc_final: 0.7378 (ttmt) REVERT: B 380 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: C 380 GLU cc_start: 0.8266 (tt0) cc_final: 0.8049 (tt0) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.4705 time to fit residues: 28.1219 Evaluate side-chains 55 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [21, 49, 35, 23, 41, 39, 42, 43, 24, 46, 4] chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146046 restraints weight = 5281.034| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.40 r_work: 0.3596 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4992 Z= 0.132 Angle : 0.595 8.577 6805 Z= 0.303 Chirality : 0.046 0.182 782 Planarity : 0.004 0.074 854 Dihedral : 5.406 40.464 811 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.00 % Allowed : 18.51 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.35), residues: 589 helix: -1.66 (0.78), residues: 43 sheet: -0.17 (0.33), residues: 262 loop : -0.73 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.011 0.001 TYR C 407 PHE 0.017 0.002 PHE C 372 TRP 0.007 0.001 TRP C 417 HIS 0.002 0.001 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 4977) covalent geometry : angle 0.58291 / 0.30 ( 6766) SS BOND : bond 0.00271 / 0.19 ( 6) SS BOND : angle 0.44332 / 0.29 ( 12) hydrogen bonds : bond 0.03243 / 2.07 ( 153) hydrogen bonds : angle 4.75987 / 3.48 ( 465) link_BETA1-4 : bond 0.00251 / 0.17 ( 4) link_BETA1-4 : angle 2.42528 / 1.25 ( 12) link_BETA1-6 : bond 0.00034 / 0.02 ( 2) link_BETA1-6 : angle 1.48683 / 0.89 ( 6) link_NAG-ASN : bond 0.00116 / 0.06 ( 3) link_NAG-ASN : angle 1.50095 / 0.85 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.183 Fit side-chains REVERT: A 148 LYS cc_start: 0.8017 (tptt) cc_final: 0.7453 (ttmt) REVERT: B 336 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8181 (tt) REVERT: B 380 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.7005 (mt-10) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.4424 time to fit residues: 24.2299 Evaluate side-chains 53 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 441 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: [38, 44, 3, 52, 40, 9, 54, 26, 34, 35, 55] chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.0020 chunk 26 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146732 restraints weight = 5284.937| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.42 r_work: 0.3628 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4992 Z= 0.109 Angle : 0.559 7.541 6805 Z= 0.286 Chirality : 0.045 0.175 782 Planarity : 0.004 0.073 854 Dihedral : 5.017 38.852 811 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.00 % Allowed : 18.87 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.82 (0.35), residues: 589 helix: -1.53 (0.79), residues: 42 sheet: -0.19 (0.32), residues: 267 loop : -0.61 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 334 TYR 0.008 0.001 TYR C 407 PHE 0.012 0.001 PHE C 372 TRP 0.005 0.001 TRP C 417 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 4977) covalent geometry : angle 0.54864 / 0.28 ( 6766) SS BOND : bond 0.00240 / 0.18 ( 6) SS BOND : angle 0.40026 / 0.26 ( 12) hydrogen bonds : bond 0.03039 / 1.97 ( 153) hydrogen bonds : angle 4.65694 / 3.40 ( 465) link_BETA1-4 : bond 0.00285 / 0.19 ( 4) link_BETA1-4 : angle 2.21001 / 1.14 ( 12) link_BETA1-6 : bond 0.00123 / 0.07 ( 2) link_BETA1-6 : angle 1.35141 / 0.82 ( 6) link_NAG-ASN : bond 0.00130 / 0.07 ( 3) link_NAG-ASN : angle 1.47532 / 0.82 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.50 seconds wall clock time: 27 minutes 47.86 seconds (1667.86 seconds total)