Starting phenix.real_space_refine on Fri Sep 11 16:14:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn2_25209/09_2026/7sn2_25209.map" } resolution = 4.3 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= 0.002 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 S 20 5.16 5 C 3284 2.51 5 N 868 2.21 5 O 1016 1.98 5 H 4904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3477 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 13, 'TRANS': 209} Chain: "H" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3236 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3251 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.04, per 1000 atoms: 0.20 Number of scatterers: 10092 At special positions: 0 Unit cell: (85.8, 113.85, 99, 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 20 16.00 O 1016 8.00 N 868 7.00 C 3284 6.00 H 4904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN C 6 " - " NAG C 7 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 331 " " NAG C 1 " - " ASN A 343 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 271.8 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.4% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.062A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.389A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.580A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.211A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.914A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.457A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.507A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.746A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 149 178 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4900 1.04 - 1.24: 685 1.24 - 1.44: 1708 1.44 - 1.64: 2905 1.64 - 1.85: 22 Bond restraints: 10220 Sorted by residual: bond pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " ideal model delta sigma weight residual 1.530 1.569 -0.039 1.58e-02 4.01e+03 6.05e+00 bond pdb=" C2 MAN C 6 " pdb=" O2 MAN C 6 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CB THR A 385 " pdb=" CG2 THR A 385 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CA ALA A 435 " pdb=" C ALA A 435 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.31e-02 5.83e+03 4.69e+00 bond pdb=" C6 BMA C 3 " pdb=" O6 BMA C 3 " ideal model delta sigma weight residual 1.411 1.453 -0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 18125 4.17 - 8.33: 159 8.33 - 12.50: 20 12.50 - 16.67: 1 16.67 - 20.84: 3 Bond angle restraints: 18308 Sorted by residual: angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 111.02 120.97 -9.95 1.22e+00 6.72e-01 6.65e+01 angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 109.97 98.40 11.57 1.47e+00 4.63e-01 6.20e+01 angle pdb=" HB2 ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB3 ASN A 437 " ideal model delta sigma weight residual 110.00 89.16 20.84 3.00e+00 1.11e-01 4.82e+01 angle pdb=" CG ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 108.00 87.44 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 109.00 88.49 20.51 3.00e+00 1.11e-01 4.67e+01 ... (remaining 18303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 4717 25.01 - 50.02: 278 50.02 - 75.03: 48 75.03 - 100.04: 17 100.04 - 125.05: 9 Dihedral angle restraints: 5069 sinusoidal: 2787 harmonic: 2282 Sorted by residual: dihedral pdb=" CA SER A 530 " pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.59 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N TYR A 396 " pdb=" CA TYR A 396 " ideal model delta harmonic sigma weight residual -180.00 -143.39 -36.61 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 756 0.118 - 0.237: 61 0.237 - 0.355: 8 0.355 - 0.474: 1 0.474 - 0.592: 1 Chirality restraints: 827 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 NAG C 7 " pdb=" O2 MAN C 6 " pdb=" C2 NAG C 7 " pdb=" O5 NAG C 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.05e+02 chirality pdb=" C1 NAG C 5 " pdb=" O2 MAN C 4 " pdb=" C2 NAG C 5 " pdb=" O5 NAG C 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.01e+02 ... (remaining 824 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 91 " 0.527 9.50e-02 1.11e+02 1.76e-01 3.40e+01 pdb=" NE ARG L 91 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 91 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG L 91 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG L 91 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 91 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 99 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ARG H 99 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG H 99 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP H 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " -0.371 9.50e-02 1.11e+02 1.24e-01 1.67e+01 pdb=" NE ARG H 94 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG H 94 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 94 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 195 2.11 - 2.73: 16965 2.73 - 3.35: 27854 3.35 - 3.98: 35537 3.98 - 4.60: 53717 Nonbonded interactions: 134268 Sorted by model distance: nonbonded pdb=" O ALA A 372 " pdb="HH22 ARG H 100D" model vdw 1.482 2.450 nonbonded pdb="HD21 ASN A 370 " pdb=" HH TYR H 58 " model vdw 1.545 2.100 nonbonded pdb="HH22 ARG A 328 " pdb=" O LYS A 528 " model vdw 1.611 2.450 nonbonded pdb=" H SER H 156 " pdb=" OD1 ASN H 197 " model vdw 1.680 2.450 nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.686 2.450 ... (remaining 134263 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.007 0.073 5334 Z= 0.329 Angle : 1.350 15.901 7282 Z= 0.720 Chirality : 0.073 0.592 827 Planarity : 0.013 0.236 916 Dihedral : 17.661 125.050 2052 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.78 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -1.92 (0.32), residues: 642 helix: -2.74 (0.79), residues: 32 sheet: -0.58 (0.35), residues: 222 loop : -1.61 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 105 TYR 0.052 0.004 TYR A 508 PHE 0.047 0.004 PHE A 329 TRP 0.032 0.003 TRP A 436 HIS 0.009 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.33 ( 5316) covalent geometry : angle 1.30779 / 0.71 ( 7236) SS BOND : bond 0.01193 / 0.58 ( 8) SS BOND : angle 2.19704 / 1.31 ( 16) hydrogen bonds : bond 0.17229 / 12.26 ( 156) hydrogen bonds : angle 10.40459 / 7.16 ( 426) link_ALPHA1-3 : bond 0.00432 / 0.23 ( 1) link_ALPHA1-3 : angle 3.77049 / 2.01 ( 3) link_ALPHA1-6 : bond 0.01257 / 0.66 ( 1) link_ALPHA1-6 : angle 5.46797 / 2.96 ( 3) link_BETA1-2 : bond 0.00930 / 0.45 ( 2) link_BETA1-2 : angle 5.10887 / 2.35 ( 6) link_BETA1-4 : bond 0.01310 / 0.68 ( 4) link_BETA1-4 : angle 5.86693 / 3.01 ( 12) link_NAG-ASN : bond 0.00753 / 0.38 ( 2) link_NAG-ASN : angle 4.37503 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7577 (m-30) REVERT: A 428 ASP cc_start: 0.8175 (t70) cc_final: 0.7962 (t70) REVERT: H 34 MET cc_start: 0.7390 (mmt) cc_final: 0.7135 (mmt) REVERT: H 46 GLU cc_start: 0.7527 (tt0) cc_final: 0.6897 (pt0) REVERT: L 13 LEU cc_start: 0.7664 (tp) cc_final: 0.7427 (tp) REVERT: L 189 HIS cc_start: 0.6327 (t-90) cc_final: 0.5909 (t70) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1593 time to fit residues: 29.3863 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.2047 > 50:) chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099987 restraints weight = 36771.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104264 restraints weight = 16171.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107033 restraints weight = 9362.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108772 restraints weight = 6450.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109724 restraints weight = 5021.390| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5334 Z= 0.150 Angle : 0.780 10.802 7282 Z= 0.400 Chirality : 0.050 0.458 827 Planarity : 0.008 0.117 916 Dihedral : 14.245 105.149 917 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.23 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.52 (0.32), residues: 642 helix: -3.47 (0.52), residues: 38 sheet: -0.05 (0.35), residues: 221 loop : -1.35 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 105 TYR 0.020 0.002 TYR A 508 PHE 0.023 0.002 PHE A 329 TRP 0.015 0.001 TRP H 100C HIS 0.005 0.002 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 5316) covalent geometry : angle 0.74957 / 0.39 ( 7236) SS BOND : bond 0.00675 / 0.29 ( 8) SS BOND : angle 0.99241 / 0.63 ( 16) hydrogen bonds : bond 0.04735 / 3.07 ( 156) hydrogen bonds : angle 8.31738 / 5.75 ( 426) link_ALPHA1-3 : bond 0.01279 / 0.67 ( 1) link_ALPHA1-3 : angle 2.43779 / 1.39 ( 3) link_ALPHA1-6 : bond 0.01444 / 0.76 ( 1) link_ALPHA1-6 : angle 0.87942 / 0.46 ( 3) link_BETA1-2 : bond 0.00305 / 0.15 ( 2) link_BETA1-2 : angle 1.23179 / 0.63 ( 6) link_BETA1-4 : bond 0.01026 / 0.50 ( 4) link_BETA1-4 : angle 4.30706 / 2.37 ( 12) link_NAG-ASN : bond 0.00632 / 0.33 ( 2) link_NAG-ASN : angle 4.08685 / 2.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7589 (m-30) REVERT: H 86 ASP cc_start: 0.9037 (m-30) cc_final: 0.8225 (m-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1604 time to fit residues: 28.8837 Evaluate side-chains 113 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096640 restraints weight = 37673.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100914 restraints weight = 16663.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103630 restraints weight = 9701.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105305 restraints weight = 6780.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106486 restraints weight = 5370.563| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5334 Z= 0.198 Angle : 0.748 11.238 7282 Z= 0.378 Chirality : 0.049 0.361 827 Planarity : 0.007 0.096 916 Dihedral : 12.960 106.282 917 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.26 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.32), residues: 642 helix: -3.20 (0.58), residues: 38 sheet: -0.22 (0.34), residues: 224 loop : -1.41 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.015 0.002 TYR L 49 PHE 0.026 0.002 PHE A 329 TRP 0.019 0.002 TRP H 100C HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 5316) covalent geometry : angle 0.71847 / 0.37 ( 7236) SS BOND : bond 0.00672 / 0.34 ( 8) SS BOND : angle 1.10838 / 0.72 ( 16) hydrogen bonds : bond 0.04191 / 2.76 ( 156) hydrogen bonds : angle 7.60331 / 5.27 ( 426) link_ALPHA1-3 : bond 0.01265 / 0.67 ( 1) link_ALPHA1-3 : angle 2.33455 / 1.32 ( 3) link_ALPHA1-6 : bond 0.01817 / 0.96 ( 1) link_ALPHA1-6 : angle 1.71024 / 0.89 ( 3) link_BETA1-2 : bond 0.00519 / 0.25 ( 2) link_BETA1-2 : angle 1.31632 / 0.66 ( 6) link_BETA1-4 : bond 0.00917 / 0.46 ( 4) link_BETA1-4 : angle 4.21749 / 2.26 ( 12) link_NAG-ASN : bond 0.00616 / 0.32 ( 2) link_NAG-ASN : angle 3.45609 / 1.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7915 (m-30) cc_final: 0.7583 (m-30) REVERT: H 86 ASP cc_start: 0.9086 (m-30) cc_final: 0.8239 (m-30) REVERT: L 185 ASP cc_start: 0.7773 (m-30) cc_final: 0.7439 (m-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1570 time to fit residues: 27.4986 Evaluate side-chains 111 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097316 restraints weight = 37342.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101517 restraints weight = 16601.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104180 restraints weight = 9733.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105924 restraints weight = 6808.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106990 restraints weight = 5338.029| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5334 Z= 0.149 Angle : 0.695 10.152 7282 Z= 0.351 Chirality : 0.047 0.336 827 Planarity : 0.006 0.087 916 Dihedral : 11.752 103.193 917 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.32), residues: 642 helix: -3.22 (0.59), residues: 38 sheet: -0.16 (0.34), residues: 223 loop : -1.38 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.021 0.001 TYR A 508 PHE 0.022 0.001 PHE A 329 TRP 0.015 0.001 TRP H 100C HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 5316) covalent geometry : angle 0.66818 / 0.35 ( 7236) SS BOND : bond 0.00879 / 0.37 ( 8) SS BOND : angle 0.67538 / 0.45 ( 16) hydrogen bonds : bond 0.03727 / 2.45 ( 156) hydrogen bonds : angle 7.20902 / 4.99 ( 426) link_ALPHA1-3 : bond 0.01211 / 0.64 ( 1) link_ALPHA1-3 : angle 2.39627 / 1.36 ( 3) link_ALPHA1-6 : bond 0.01845 / 0.97 ( 1) link_ALPHA1-6 : angle 2.33373 / 1.22 ( 3) link_BETA1-2 : bond 0.00550 / 0.27 ( 2) link_BETA1-2 : angle 1.08211 / 0.56 ( 6) link_BETA1-4 : bond 0.00816 / 0.40 ( 4) link_BETA1-4 : angle 3.86654 / 2.08 ( 12) link_NAG-ASN : bond 0.00560 / 0.29 ( 2) link_NAG-ASN : angle 3.09396 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7941 (m-30) cc_final: 0.7614 (m-30) REVERT: H 86 ASP cc_start: 0.9127 (m-30) cc_final: 0.8266 (m-30) REVERT: L 174 SER cc_start: 0.9370 (t) cc_final: 0.9143 (t) REVERT: L 185 ASP cc_start: 0.7805 (m-30) cc_final: 0.7476 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1545 time to fit residues: 25.7940 Evaluate side-chains 106 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098136 restraints weight = 36993.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102533 restraints weight = 16128.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105291 restraints weight = 9324.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107039 restraints weight = 6461.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108180 restraints weight = 5061.993| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5334 Z= 0.126 Angle : 0.678 9.567 7282 Z= 0.341 Chirality : 0.047 0.339 827 Planarity : 0.006 0.074 916 Dihedral : 10.690 98.458 917 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.44 (0.33), residues: 642 helix: -3.21 (0.58), residues: 38 sheet: -0.03 (0.34), residues: 222 loop : -1.31 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.020 0.001 TYR A 508 PHE 0.023 0.001 PHE L 62 TRP 0.016 0.001 TRP H 100C HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5316) covalent geometry : angle 0.65268 / 0.34 ( 7236) SS BOND : bond 0.00626 / 0.24 ( 8) SS BOND : angle 0.63983 / 0.40 ( 16) hydrogen bonds : bond 0.03486 / 2.29 ( 156) hydrogen bonds : angle 6.86350 / 4.76 ( 426) link_ALPHA1-3 : bond 0.01349 / 0.71 ( 1) link_ALPHA1-3 : angle 2.49666 / 1.41 ( 3) link_ALPHA1-6 : bond 0.01610 / 0.85 ( 1) link_ALPHA1-6 : angle 3.02663 / 1.58 ( 3) link_BETA1-2 : bond 0.00255 / 0.12 ( 2) link_BETA1-2 : angle 0.73376 / 0.36 ( 6) link_BETA1-4 : bond 0.00661 / 0.33 ( 4) link_BETA1-4 : angle 3.60200 / 1.91 ( 12) link_NAG-ASN : bond 0.00422 / 0.22 ( 2) link_NAG-ASN : angle 2.84206 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7902 (m-30) cc_final: 0.7575 (m-30) REVERT: H 86 ASP cc_start: 0.9144 (m-30) cc_final: 0.8259 (m-30) REVERT: H 206 LYS cc_start: 0.8374 (tptp) cc_final: 0.8130 (tptp) REVERT: L 174 SER cc_start: 0.9324 (t) cc_final: 0.9074 (t) REVERT: L 185 ASP cc_start: 0.7813 (m-30) cc_final: 0.7514 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1661 time to fit residues: 27.9020 Evaluate side-chains 108 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096260 restraints weight = 37373.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100538 restraints weight = 16500.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103282 restraints weight = 9647.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105005 restraints weight = 6733.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106132 restraints weight = 5311.390| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5334 Z= 0.159 Angle : 0.688 9.236 7282 Z= 0.345 Chirality : 0.047 0.337 827 Planarity : 0.006 0.112 916 Dihedral : 10.328 94.337 917 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.46 (0.33), residues: 642 helix: -3.20 (0.58), residues: 38 sheet: -0.01 (0.34), residues: 222 loop : -1.34 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.022 0.002 TYR A 508 PHE 0.021 0.001 PHE A 329 TRP 0.017 0.001 TRP H 100C HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 5316) covalent geometry : angle 0.66357 / 0.34 ( 7236) SS BOND : bond 0.00628 / 0.26 ( 8) SS BOND : angle 0.88838 / 0.57 ( 16) hydrogen bonds : bond 0.03391 / 2.23 ( 156) hydrogen bonds : angle 6.73013 / 4.66 ( 426) link_ALPHA1-3 : bond 0.01386 / 0.73 ( 1) link_ALPHA1-3 : angle 2.63341 / 1.46 ( 3) link_ALPHA1-6 : bond 0.02019 / 1.06 ( 1) link_ALPHA1-6 : angle 2.87744 / 1.50 ( 3) link_BETA1-2 : bond 0.00320 / 0.16 ( 2) link_BETA1-2 : angle 0.78008 / 0.43 ( 6) link_BETA1-4 : bond 0.00548 / 0.27 ( 4) link_BETA1-4 : angle 3.55257 / 1.95 ( 12) link_NAG-ASN : bond 0.00465 / 0.24 ( 2) link_NAG-ASN : angle 2.85588 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7866 (m-30) cc_final: 0.7531 (m-30) REVERT: A 509 ARG cc_start: 0.7513 (ttt90) cc_final: 0.7229 (ttt90) REVERT: H 46 GLU cc_start: 0.7717 (tt0) cc_final: 0.7023 (pt0) REVERT: H 86 ASP cc_start: 0.9112 (m-30) cc_final: 0.8252 (m-30) REVERT: H 95 ASP cc_start: 0.7487 (t0) cc_final: 0.7269 (t0) REVERT: H 117 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8040 (ptmm) REVERT: H 206 LYS cc_start: 0.8441 (tptp) cc_final: 0.7946 (tptp) REVERT: L 174 SER cc_start: 0.9352 (t) cc_final: 0.9105 (t) REVERT: L 185 ASP cc_start: 0.7960 (m-30) cc_final: 0.7690 (m-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1834 time to fit residues: 30.4635 Evaluate side-chains 107 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094598 restraints weight = 37392.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098884 restraints weight = 16906.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101640 restraints weight = 10025.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103459 restraints weight = 7050.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104435 restraints weight = 5560.123| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5334 Z= 0.175 Angle : 0.697 8.930 7282 Z= 0.350 Chirality : 0.046 0.326 827 Planarity : 0.006 0.051 916 Dihedral : 10.019 86.050 917 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.63 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 642 helix: -3.20 (0.59), residues: 38 sheet: -0.11 (0.35), residues: 222 loop : -1.42 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.018 0.002 TYR A 508 PHE 0.022 0.002 PHE A 329 TRP 0.016 0.002 TRP H 100C HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 5316) covalent geometry : angle 0.67345 / 0.34 ( 7236) SS BOND : bond 0.00622 / 0.26 ( 8) SS BOND : angle 0.86322 / 0.55 ( 16) hydrogen bonds : bond 0.03288 / 2.15 ( 156) hydrogen bonds : angle 6.60555 / 4.58 ( 426) link_ALPHA1-3 : bond 0.01464 / 0.77 ( 1) link_ALPHA1-3 : angle 2.83917 / 1.55 ( 3) link_ALPHA1-6 : bond 0.02154 / 1.13 ( 1) link_ALPHA1-6 : angle 2.91443 / 1.52 ( 3) link_BETA1-2 : bond 0.00418 / 0.21 ( 2) link_BETA1-2 : angle 0.88676 / 0.50 ( 6) link_BETA1-4 : bond 0.00482 / 0.24 ( 4) link_BETA1-4 : angle 3.44781 / 1.93 ( 12) link_NAG-ASN : bond 0.00493 / 0.26 ( 2) link_NAG-ASN : angle 2.83328 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7891 (m-30) cc_final: 0.7560 (m-30) REVERT: H 86 ASP cc_start: 0.9152 (m-30) cc_final: 0.8283 (m-30) REVERT: H 123 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8963 (Cg_endo) REVERT: H 206 LYS cc_start: 0.8460 (tptp) cc_final: 0.8040 (tptp) REVERT: L 93 ASN cc_start: 0.8389 (p0) cc_final: 0.7743 (t0) REVERT: L 174 SER cc_start: 0.9355 (t) cc_final: 0.9108 (t) REVERT: L 185 ASP cc_start: 0.8070 (m-30) cc_final: 0.7804 (m-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1853 time to fit residues: 30.1951 Evaluate side-chains 100 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095676 restraints weight = 36754.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099964 restraints weight = 16278.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102715 restraints weight = 9475.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104476 restraints weight = 6580.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105475 restraints weight = 5158.701| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5334 Z= 0.123 Angle : 0.667 8.609 7282 Z= 0.333 Chirality : 0.046 0.305 827 Planarity : 0.006 0.075 916 Dihedral : 9.324 78.949 917 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.33), residues: 642 helix: -3.13 (0.61), residues: 38 sheet: -0.07 (0.35), residues: 222 loop : -1.36 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 105 TYR 0.016 0.001 TYR L 36 PHE 0.021 0.001 PHE A 329 TRP 0.015 0.001 TRP H 100C HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5316) covalent geometry : angle 0.64330 / 0.33 ( 7236) SS BOND : bond 0.00609 / 0.24 ( 8) SS BOND : angle 0.75663 / 0.47 ( 16) hydrogen bonds : bond 0.03275 / 2.16 ( 156) hydrogen bonds : angle 6.48354 / 4.49 ( 426) link_ALPHA1-3 : bond 0.01571 / 0.83 ( 1) link_ALPHA1-3 : angle 2.94980 / 1.59 ( 3) link_ALPHA1-6 : bond 0.02167 / 1.14 ( 1) link_ALPHA1-6 : angle 3.42957 / 1.79 ( 3) link_BETA1-2 : bond 0.00448 / 0.22 ( 2) link_BETA1-2 : angle 0.73157 / 0.40 ( 6) link_BETA1-4 : bond 0.00523 / 0.26 ( 4) link_BETA1-4 : angle 3.28069 / 1.82 ( 12) link_NAG-ASN : bond 0.00342 / 0.18 ( 2) link_NAG-ASN : angle 2.53403 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7828 (m-30) cc_final: 0.7510 (m-30) REVERT: H 86 ASP cc_start: 0.9191 (m-30) cc_final: 0.8537 (m-30) REVERT: L 174 SER cc_start: 0.9310 (t) cc_final: 0.9053 (t) REVERT: L 185 ASP cc_start: 0.8002 (m-30) cc_final: 0.7749 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1806 time to fit residues: 29.7772 Evaluate side-chains 102 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096685 restraints weight = 36699.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101029 restraints weight = 16239.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103858 restraints weight = 9457.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105498 restraints weight = 6576.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106744 restraints weight = 5226.070| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5334 Z= 0.121 Angle : 0.661 8.327 7282 Z= 0.330 Chirality : 0.046 0.306 827 Planarity : 0.006 0.048 916 Dihedral : 8.605 64.840 917 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.42 (0.33), residues: 642 helix: -3.03 (0.64), residues: 38 sheet: 0.02 (0.35), residues: 222 loop : -1.34 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.019 0.001 TYR A 508 PHE 0.021 0.001 PHE A 329 TRP 0.015 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5316) covalent geometry : angle 0.63759 / 0.33 ( 7236) SS BOND : bond 0.00573 / 0.23 ( 8) SS BOND : angle 0.76013 / 0.49 ( 16) hydrogen bonds : bond 0.03233 / 2.12 ( 156) hydrogen bonds : angle 6.33494 / 4.39 ( 426) link_ALPHA1-3 : bond 0.01761 / 0.93 ( 1) link_ALPHA1-3 : angle 3.30625 / 1.72 ( 3) link_ALPHA1-6 : bond 0.02218 / 1.17 ( 1) link_ALPHA1-6 : angle 3.50491 / 1.83 ( 3) link_BETA1-2 : bond 0.00356 / 0.18 ( 2) link_BETA1-2 : angle 0.75757 / 0.43 ( 6) link_BETA1-4 : bond 0.00482 / 0.24 ( 4) link_BETA1-4 : angle 3.20022 / 1.80 ( 12) link_NAG-ASN : bond 0.00323 / 0.17 ( 2) link_NAG-ASN : angle 2.40180 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7844 (m-30) cc_final: 0.7469 (m-30) REVERT: H 46 GLU cc_start: 0.7617 (tt0) cc_final: 0.6720 (pt0) REVERT: H 86 ASP cc_start: 0.9219 (m-30) cc_final: 0.8618 (m-30) REVERT: H 117 LYS cc_start: 0.8448 (ptmt) cc_final: 0.8061 (ptmm) REVERT: L 174 SER cc_start: 0.9280 (t) cc_final: 0.9018 (t) REVERT: L 185 ASP cc_start: 0.7945 (m-30) cc_final: 0.7699 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1847 time to fit residues: 30.1995 Evaluate side-chains 106 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095791 restraints weight = 36667.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100056 restraints weight = 16239.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102829 restraints weight = 9444.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104617 restraints weight = 6573.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105779 restraints weight = 5151.704| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5334 Z= 0.134 Angle : 0.658 8.254 7282 Z= 0.327 Chirality : 0.046 0.309 827 Planarity : 0.005 0.050 916 Dihedral : 8.140 50.492 917 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.46 (0.33), residues: 642 helix: -3.01 (0.64), residues: 38 sheet: 0.02 (0.35), residues: 222 loop : -1.39 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 105 TYR 0.013 0.001 TYR L 36 PHE 0.020 0.001 PHE A 329 TRP 0.014 0.001 TRP H 100C HIS 0.002 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5316) covalent geometry : angle 0.63200 / 0.32 ( 7236) SS BOND : bond 0.00570 / 0.23 ( 8) SS BOND : angle 0.78922 / 0.52 ( 16) hydrogen bonds : bond 0.03184 / 2.06 ( 156) hydrogen bonds : angle 6.26912 / 4.35 ( 426) link_ALPHA1-3 : bond 0.01817 / 0.96 ( 1) link_ALPHA1-3 : angle 3.86937 / 1.99 ( 3) link_ALPHA1-6 : bond 0.02302 / 1.21 ( 1) link_ALPHA1-6 : angle 3.46981 / 1.81 ( 3) link_BETA1-2 : bond 0.00281 / 0.14 ( 2) link_BETA1-2 : angle 1.02047 / 0.57 ( 6) link_BETA1-4 : bond 0.00457 / 0.23 ( 4) link_BETA1-4 : angle 3.24982 / 1.85 ( 12) link_NAG-ASN : bond 0.00354 / 0.19 ( 2) link_NAG-ASN : angle 2.45516 / 1.33 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7800 (m-30) cc_final: 0.7450 (m-30) REVERT: H 46 GLU cc_start: 0.7623 (tt0) cc_final: 0.6656 (pt0) REVERT: H 86 ASP cc_start: 0.9225 (m-30) cc_final: 0.8623 (m-30) REVERT: H 117 LYS cc_start: 0.8461 (ptmt) cc_final: 0.8172 (ptmm) REVERT: L 174 SER cc_start: 0.9297 (t) cc_final: 0.9038 (t) REVERT: L 185 ASP cc_start: 0.7960 (m-30) cc_final: 0.7710 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1816 time to fit residues: 29.1077 Evaluate side-chains 109 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095648 restraints weight = 37505.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099969 restraints weight = 16603.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102763 restraints weight = 9708.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104561 restraints weight = 6768.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105529 restraints weight = 5332.957| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5334 Z= 0.124 Angle : 0.656 8.108 7282 Z= 0.327 Chirality : 0.046 0.291 827 Planarity : 0.005 0.049 916 Dihedral : 7.846 49.195 917 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.39 (0.33), residues: 642 helix: -2.97 (0.66), residues: 38 sheet: 0.07 (0.35), residues: 222 loop : -1.35 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 105 TYR 0.018 0.001 TYR A 508 PHE 0.020 0.001 PHE A 329 TRP 0.013 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5316) covalent geometry : angle 0.63030 / 0.32 ( 7236) SS BOND : bond 0.00577 / 0.23 ( 8) SS BOND : angle 0.96752 / 0.59 ( 16) hydrogen bonds : bond 0.03163 / 2.07 ( 156) hydrogen bonds : angle 6.17639 / 4.29 ( 426) link_ALPHA1-3 : bond 0.01852 / 0.97 ( 1) link_ALPHA1-3 : angle 3.90557 / 2.01 ( 3) link_ALPHA1-6 : bond 0.02384 / 1.25 ( 1) link_ALPHA1-6 : angle 3.66957 / 1.92 ( 3) link_BETA1-2 : bond 0.00308 / 0.15 ( 2) link_BETA1-2 : angle 1.15202 / 0.64 ( 6) link_BETA1-4 : bond 0.00468 / 0.24 ( 4) link_BETA1-4 : angle 3.16233 / 1.76 ( 12) link_NAG-ASN : bond 0.00355 / 0.19 ( 2) link_NAG-ASN : angle 2.37326 / 1.28 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.79 seconds wall clock time: 36 minutes 47.30 seconds (2207.30 seconds total)