Starting phenix.real_space_refine on Thu Jul 2 01:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgm_34742/07_2026/8hgm_34742.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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 22 5.16 5 C 3085 2.51 5 N 820 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4886 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1532 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.13, per 1000 atoms: 0.23 Number of scatterers: 4886 At special positions: 0 Unit cell: (72.726, 70.38, 136.068, 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 22 16.00 O 959 8.00 N 820 7.00 C 3085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 191.7 milliseconds 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 12.7% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.976A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.574A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.277A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 26 through 29 removed outlier: 3.794A pdb=" N TYR C 29 " --> pdb=" O THR C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'D' and resid 80 through 84 removed outlier: 4.009A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.772A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.860A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 189' Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.598A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.630A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.827A pdb=" N GLY C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 36 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP C 45 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.545A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.545A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.668A pdb=" N THR C 159 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 204 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.720A pdb=" N LEU D 74 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.823A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 119 removed outlier: 6.231A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 179 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 154 through 155 removed outlier: 3.549A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 450 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: 0.72 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1563 1.34 - 1.46: 1257 1.46 - 1.58: 2162 1.58 - 1.70: 0 1.70 - 1.81: 25 Bond restraints: 5007 Sorted by residual: bond pdb=" C THR C 173 " pdb=" N PHE C 174 " ideal model delta sigma weight residual 1.333 1.289 0.043 2.74e-02 1.33e+03 2.50e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.425 -0.019 2.00e-02 2.50e+03 9.20e-01 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 6769 2.86 - 5.73: 40 5.73 - 8.59: 2 8.59 - 11.45: 0 11.45 - 14.31: 1 Bond angle restraints: 6812 Sorted by residual: angle pdb=" C LYS C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 122.82 126.84 -4.02 1.42e+00 4.96e-01 8.00e+00 angle pdb=" C THR C 173 " pdb=" N PHE C 174 " pdb=" CA PHE C 174 " ideal model delta sigma weight residual 122.15 113.71 8.44 3.47e+00 8.31e-02 5.91e+00 angle pdb=" C LYS C 10 " pdb=" N LYS C 11 " pdb=" CA LYS C 11 " ideal model delta sigma weight residual 120.71 135.02 -14.31 6.53e+00 2.35e-02 4.81e+00 angle pdb=" N TYR D 92 " pdb=" CA TYR D 92 " pdb=" C TYR D 92 " ideal model delta sigma weight residual 110.88 113.57 -2.69 1.28e+00 6.10e-01 4.41e+00 angle pdb=" C GLY D 51 " pdb=" N THR D 52 " pdb=" CA THR D 52 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.95e+00 ... (remaining 6807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2717 17.76 - 35.51: 205 35.51 - 53.27: 38 53.27 - 71.03: 7 71.03 - 88.78: 3 Dihedral angle restraints: 2970 sinusoidal: 1142 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -55.63 -30.37 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA CYS C 99 " pdb=" CB CYS C 99 " pdb=" SG CYS C 99 " pdb=" SG CYS C 104 " ideal model delta sinusoidal sigma weight residual -73.00 -10.05 -62.95 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" CA LEU B 461 " pdb=" C LEU B 461 " pdb=" N LYS B 462 " pdb=" CA LYS B 462 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 473 0.033 - 0.066: 183 0.066 - 0.099: 58 0.099 - 0.132: 37 0.132 - 0.165: 1 Chirality restraints: 752 Sorted by residual: chirality pdb=" CA ASP C 152 " pdb=" N ASP C 152 " pdb=" C ASP C 152 " pdb=" CB ASP C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA SER D 7 " pdb=" N SER D 7 " pdb=" C SER D 7 " pdb=" CB SER D 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 749 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO B 521 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 186 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.43e+00 pdb=" CG ASP D 186 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP D 186 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP D 186 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 463 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.015 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 230 2.72 - 3.27: 4720 3.27 - 3.81: 7543 3.81 - 4.36: 8788 4.36 - 4.90: 15508 Nonbonded interactions: 36789 Sorted by model distance: nonbonded pdb=" OG SER B 371 " pdb=" OG SER B 373 " model vdw 2.180 3.040 nonbonded pdb=" OG SER C 211 " pdb=" OG1 THR C 213 " model vdw 2.213 3.040 nonbonded pdb=" NE2 GLN C 179 " pdb=" O LEU C 183 " model vdw 2.229 3.120 nonbonded pdb=" OD2 ASP D 152 " pdb=" ND1 HIS D 190 " model vdw 2.256 3.120 nonbonded pdb=" OG SER B 375 " pdb=" O ALA B 435 " model vdw 2.289 3.040 ... (remaining 36784 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.004 0.043 5018 Z= 0.156 Angle : 0.590 14.314 6836 Z= 0.291 Chirality : 0.043 0.165 752 Planarity : 0.004 0.046 879 Dihedral : 13.054 88.784 1779 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.35), residues: 626 helix: -2.00 (0.80), residues: 33 sheet: 1.03 (0.35), residues: 243 loop : -0.14 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 346 TYR 0.016 0.001 TYR C 105 PHE 0.008 0.001 PHE D 140 TRP 0.004 0.001 TRP D 149 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 5007) covalent geometry : angle 0.58837 / 0.29 ( 6812) SS BOND : bond 0.00400 / 0.22 ( 9) SS BOND : angle 0.68148 / 0.39 ( 18) hydrogen bonds : bond 0.27833 / 18.44 ( 158) hydrogen bonds : angle 10.08560 / 7.47 ( 450) link_BETA1-4 : bond 0.00139 / 0.07 ( 1) link_BETA1-4 : angle 1.22620 / 1.11 ( 3) link_NAG-ASN : bond 0.00243 / 0.13 ( 1) link_NAG-ASN : angle 1.72699 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.7749 (t0) cc_final: 0.7189 (t0) REVERT: D 43 GLN cc_start: 0.7679 (mp10) cc_final: 0.7350 (mp10) REVERT: D 82 GLU cc_start: 0.8272 (pm20) cc_final: 0.7946 (pm20) REVERT: D 107 ILE cc_start: 0.9195 (mt) cc_final: 0.8973 (tt) REVERT: D 125 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7749 (tp-100) REVERT: D 150 LYS cc_start: 0.7857 (tppt) cc_final: 0.7629 (tmtt) REVERT: D 168 ASP cc_start: 0.9005 (t70) cc_final: 0.8672 (t70) REVERT: D 182 LEU cc_start: 0.9221 (tp) cc_final: 0.8930 (tt) REVERT: D 211 ASN cc_start: 0.8587 (t0) cc_final: 0.8235 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0890 time to fit residues: 9.4314 Evaluate side-chains 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.081881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060878 restraints weight = 13880.400| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.21 r_work: 0.2861 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5018 Z= 0.132 Angle : 0.607 13.423 6836 Z= 0.310 Chirality : 0.044 0.176 752 Planarity : 0.004 0.047 879 Dihedral : 4.443 24.772 690 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.30 % Allowed : 7.42 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.34), residues: 626 helix: -2.20 (0.67), residues: 39 sheet: 0.90 (0.34), residues: 238 loop : -0.11 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.025 0.001 TYR C 153 PHE 0.008 0.001 PHE B 400 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5007) covalent geometry : angle 0.60521 / 0.31 ( 6812) SS BOND : bond 0.00598 / 0.35 ( 9) SS BOND : angle 1.00537 / 0.48 ( 18) hydrogen bonds : bond 0.04139 / 2.71 ( 158) hydrogen bonds : angle 6.77165 / 4.98 ( 450) link_BETA1-4 : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : angle 1.07372 / 0.95 ( 3) link_NAG-ASN : bond 0.00066 / 0.03 ( 1) link_NAG-ASN : angle 1.39487 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.7152 (t0) cc_final: 0.6484 (t0) REVERT: C 72 MET cc_start: 0.8985 (tpp) cc_final: 0.8764 (mpp) REVERT: C 105 TYR cc_start: 0.8962 (t80) cc_final: 0.8707 (t80) REVERT: D 43 GLN cc_start: 0.7551 (mp10) cc_final: 0.7174 (mp10) REVERT: D 82 GLU cc_start: 0.8733 (pm20) cc_final: 0.8419 (pm20) REVERT: D 139 ASN cc_start: 0.8184 (t0) cc_final: 0.7874 (m-40) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.0719 time to fit residues: 6.2358 Evaluate side-chains 63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.060957 restraints weight = 13924.645| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.25 r_work: 0.2868 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5018 Z= 0.117 Angle : 0.579 13.171 6836 Z= 0.288 Chirality : 0.043 0.195 752 Planarity : 0.004 0.048 879 Dihedral : 4.280 23.605 690 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.67 % Allowed : 9.28 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.34), residues: 626 helix: -2.06 (0.69), residues: 39 sheet: 1.08 (0.35), residues: 235 loop : 0.02 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.025 0.001 TYR C 153 PHE 0.012 0.001 PHE C 130 TRP 0.006 0.001 TRP C 162 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5007) covalent geometry : angle 0.57750 / 0.29 ( 6812) SS BOND : bond 0.00462 / 0.28 ( 9) SS BOND : angle 0.88609 / 0.44 ( 18) hydrogen bonds : bond 0.03567 / 2.26 ( 158) hydrogen bonds : angle 5.96655 / 4.39 ( 450) link_BETA1-4 : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : angle 0.92549 / 0.80 ( 3) link_NAG-ASN : bond 0.00043 / 0.02 ( 1) link_NAG-ASN : angle 1.33181 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8916 (tp30) cc_final: 0.8501 (mm-30) REVERT: B 465 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: B 471 GLU cc_start: 0.8714 (tp30) cc_final: 0.8484 (tp30) REVERT: C 71 ASP cc_start: 0.7068 (t0) cc_final: 0.6415 (t0) REVERT: C 72 MET cc_start: 0.8884 (tpp) cc_final: 0.8655 (mpp) REVERT: C 105 TYR cc_start: 0.8910 (t80) cc_final: 0.7952 (t80) REVERT: C 106 ASP cc_start: 0.9375 (t0) cc_final: 0.9052 (t0) REVERT: D 43 GLN cc_start: 0.7559 (mp10) cc_final: 0.7163 (mp10) REVERT: D 80 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8383 (mm-30) REVERT: D 82 GLU cc_start: 0.8769 (pm20) cc_final: 0.8426 (pm20) REVERT: D 125 GLN cc_start: 0.8268 (tp40) cc_final: 0.7778 (mm-40) REVERT: D 162 GLU cc_start: 0.9144 (tp30) cc_final: 0.8943 (tp30) REVERT: D 189 LYS cc_start: 0.8905 (pptt) cc_final: 0.8657 (ptmm) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.0746 time to fit residues: 6.7296 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 46 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061725 restraints weight = 13948.145| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.35 r_work: 0.2884 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5018 Z= 0.098 Angle : 0.553 12.998 6836 Z= 0.272 Chirality : 0.042 0.172 752 Planarity : 0.004 0.047 879 Dihedral : 4.160 22.152 690 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.67 % Allowed : 11.32 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.35), residues: 626 helix: -1.84 (0.73), residues: 39 sheet: 1.10 (0.34), residues: 237 loop : 0.10 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.027 0.001 TYR C 153 PHE 0.007 0.001 PHE C 130 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.000 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 5007) covalent geometry : angle 0.55106 / 0.27 ( 6812) SS BOND : bond 0.00473 / 0.28 ( 9) SS BOND : angle 0.91643 / 0.48 ( 18) hydrogen bonds : bond 0.02960 / 1.88 ( 158) hydrogen bonds : angle 5.51193 / 4.07 ( 450) link_BETA1-4 : bond 0.00186 / 0.10 ( 1) link_BETA1-4 : angle 0.85271 / 0.74 ( 3) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 1.20524 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: B 471 GLU cc_start: 0.8724 (tp30) cc_final: 0.8452 (tp30) REVERT: C 71 ASP cc_start: 0.6984 (t0) cc_final: 0.6369 (t0) REVERT: C 105 TYR cc_start: 0.8877 (t80) cc_final: 0.7914 (t80) REVERT: C 106 ASP cc_start: 0.9381 (t0) cc_final: 0.9056 (t0) REVERT: D 43 GLN cc_start: 0.7467 (mp10) cc_final: 0.6883 (mp10) REVERT: D 189 LYS cc_start: 0.8905 (pptt) cc_final: 0.8647 (ptmm) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0689 time to fit residues: 5.9348 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.060464 restraints weight = 13985.389| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.27 r_work: 0.2857 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5018 Z= 0.136 Angle : 0.580 13.419 6836 Z= 0.285 Chirality : 0.043 0.190 752 Planarity : 0.004 0.048 879 Dihedral : 4.232 21.451 690 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.23 % Allowed : 11.69 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.35), residues: 626 helix: -1.97 (0.72), residues: 39 sheet: 1.15 (0.34), residues: 243 loop : 0.08 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.026 0.001 TYR C 153 PHE 0.009 0.001 PHE D 140 TRP 0.006 0.001 TRP C 162 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5007) covalent geometry : angle 0.57732 / 0.28 ( 6812) SS BOND : bond 0.00444 / 0.27 ( 9) SS BOND : angle 0.92773 / 0.46 ( 18) hydrogen bonds : bond 0.03166 / 1.98 ( 158) hydrogen bonds : angle 5.37404 / 3.99 ( 450) link_BETA1-4 : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : angle 1.07355 / 0.96 ( 3) link_NAG-ASN : bond 0.00263 / 0.14 ( 1) link_NAG-ASN : angle 1.53564 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8431 (mt-10) REVERT: B 465 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: C 71 ASP cc_start: 0.7077 (t0) cc_final: 0.6448 (t0) REVERT: C 105 TYR cc_start: 0.8900 (t80) cc_final: 0.8023 (t80) REVERT: C 106 ASP cc_start: 0.9428 (t0) cc_final: 0.9075 (t0) REVERT: D 43 GLN cc_start: 0.7533 (mp10) cc_final: 0.6921 (mp10) REVERT: D 189 LYS cc_start: 0.8892 (pptt) cc_final: 0.8621 (ptmm) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.0680 time to fit residues: 5.6371 Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060868 restraints weight = 14244.148| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.39 r_work: 0.2866 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5018 Z= 0.113 Angle : 0.569 13.159 6836 Z= 0.278 Chirality : 0.042 0.176 752 Planarity : 0.004 0.047 879 Dihedral : 4.154 21.890 690 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 13.17 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.35), residues: 626 helix: -1.98 (0.71), residues: 39 sheet: 1.13 (0.35), residues: 238 loop : 0.20 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.027 0.001 TYR C 153 PHE 0.007 0.001 PHE D 140 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 5007) covalent geometry : angle 0.56722 / 0.28 ( 6812) SS BOND : bond 0.00390 / 0.24 ( 9) SS BOND : angle 0.88196 / 0.44 ( 18) hydrogen bonds : bond 0.02846 / 1.80 ( 158) hydrogen bonds : angle 5.22605 / 3.87 ( 450) link_BETA1-4 : bond 0.00037 / 0.02 ( 1) link_BETA1-4 : angle 0.84370 / 0.72 ( 3) link_NAG-ASN : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : angle 1.32205 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8376 (mt-10) REVERT: B 465 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: C 71 ASP cc_start: 0.7050 (t0) cc_final: 0.6447 (t0) REVERT: C 105 TYR cc_start: 0.8926 (t80) cc_final: 0.8101 (t80) REVERT: C 106 ASP cc_start: 0.9440 (t0) cc_final: 0.9081 (t0) REVERT: D 43 GLN cc_start: 0.7465 (mp10) cc_final: 0.6887 (mp10) REVERT: D 189 LYS cc_start: 0.8900 (pptt) cc_final: 0.8614 (ptmm) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.0632 time to fit residues: 5.2385 Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 45 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3400 r_free = 0.3400 target = 0.082608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.061128 restraints weight = 14022.245| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.37 r_work: 0.2873 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5018 Z= 0.107 Angle : 0.564 13.161 6836 Z= 0.275 Chirality : 0.042 0.173 752 Planarity : 0.004 0.047 879 Dihedral : 4.078 21.956 690 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.23 % Allowed : 13.73 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.35), residues: 626 helix: -1.89 (0.72), residues: 39 sheet: 1.14 (0.35), residues: 237 loop : 0.21 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.026 0.001 TYR C 153 PHE 0.007 0.001 PHE D 140 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 5007) covalent geometry : angle 0.56255 / 0.27 ( 6812) SS BOND : bond 0.00364 / 0.23 ( 9) SS BOND : angle 0.85106 / 0.42 ( 18) hydrogen bonds : bond 0.02762 / 1.74 ( 158) hydrogen bonds : angle 5.16166 / 3.83 ( 450) link_BETA1-4 : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : angle 0.90591 / 0.79 ( 3) link_NAG-ASN : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : angle 1.32522 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8328 (mt-10) REVERT: B 465 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: C 71 ASP cc_start: 0.7002 (t0) cc_final: 0.6379 (t0) REVERT: C 105 TYR cc_start: 0.8915 (t80) cc_final: 0.8143 (t80) REVERT: C 106 ASP cc_start: 0.9455 (t0) cc_final: 0.9095 (t0) REVERT: D 43 GLN cc_start: 0.7428 (mp10) cc_final: 0.6876 (mp10) REVERT: D 189 LYS cc_start: 0.8898 (pptt) cc_final: 0.8584 (ptmm) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.0556 time to fit residues: 5.1734 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.079487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058231 restraints weight = 14183.838| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.27 r_work: 0.2812 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5018 Z= 0.229 Angle : 0.658 14.075 6836 Z= 0.325 Chirality : 0.045 0.203 752 Planarity : 0.004 0.047 879 Dihedral : 4.545 22.515 690 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.97 % Allowed : 13.73 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.35), residues: 626 helix: -2.54 (0.66), residues: 39 sheet: 1.06 (0.35), residues: 241 loop : 0.04 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 346 TYR 0.028 0.002 TYR C 153 PHE 0.013 0.001 PHE D 140 TRP 0.008 0.001 TRP D 149 HIS 0.003 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 5007) covalent geometry : angle 0.65555 / 0.32 ( 6812) SS BOND : bond 0.00544 / 0.30 ( 9) SS BOND : angle 1.02059 / 0.49 ( 18) hydrogen bonds : bond 0.03648 / 2.30 ( 158) hydrogen bonds : angle 5.42047 / 4.05 ( 450) link_BETA1-4 : bond 0.00523 / 0.28 ( 1) link_BETA1-4 : angle 1.30258 / 1.22 ( 3) link_NAG-ASN : bond 0.00555 / 0.29 ( 1) link_NAG-ASN : angle 1.94188 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8365 (mt-10) REVERT: B 465 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: B 467 ASP cc_start: 0.8397 (m-30) cc_final: 0.7890 (m-30) REVERT: C 105 TYR cc_start: 0.8994 (t80) cc_final: 0.8317 (t80) REVERT: C 220 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 43 GLN cc_start: 0.7626 (mp10) cc_final: 0.6973 (mp10) REVERT: D 189 LYS cc_start: 0.8898 (pptt) cc_final: 0.8581 (ptmm) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.0637 time to fit residues: 5.4339 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3377 r_free = 0.3377 target = 0.081259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059929 restraints weight = 13856.191| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.24 r_work: 0.2852 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5018 Z= 0.128 Angle : 0.610 13.728 6836 Z= 0.295 Chirality : 0.043 0.186 752 Planarity : 0.004 0.046 879 Dihedral : 4.319 22.884 690 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 15.58 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.35), residues: 626 helix: -2.27 (0.68), residues: 39 sheet: 1.01 (0.35), residues: 236 loop : 0.12 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.029 0.001 TYR C 153 PHE 0.007 0.001 PHE D 140 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 5007) covalent geometry : angle 0.60780 / 0.29 ( 6812) SS BOND : bond 0.00407 / 0.24 ( 9) SS BOND : angle 0.93771 / 0.47 ( 18) hydrogen bonds : bond 0.02979 / 1.87 ( 158) hydrogen bonds : angle 5.25573 / 3.90 ( 450) link_BETA1-4 : bond 0.00146 / 0.08 ( 1) link_BETA1-4 : angle 0.87797 / 0.76 ( 3) link_NAG-ASN : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : angle 1.46496 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8455 (mt-10) REVERT: B 465 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: C 105 TYR cc_start: 0.8968 (t80) cc_final: 0.8274 (t80) REVERT: C 220 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6948 (mm-30) REVERT: D 43 GLN cc_start: 0.7536 (mp10) cc_final: 0.6932 (mp10) REVERT: D 189 LYS cc_start: 0.8887 (pptt) cc_final: 0.8569 (ptmm) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.0657 time to fit residues: 5.6710 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.081386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.060138 restraints weight = 14069.218| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.28 r_work: 0.2854 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5018 Z= 0.129 Angle : 0.616 13.618 6836 Z= 0.298 Chirality : 0.043 0.178 752 Planarity : 0.004 0.046 879 Dihedral : 4.223 23.100 690 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.23 % Allowed : 15.40 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.35), residues: 626 helix: -2.28 (0.67), residues: 39 sheet: 1.02 (0.35), residues: 236 loop : 0.13 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.028 0.001 TYR C 153 PHE 0.008 0.001 PHE D 140 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5007) covalent geometry : angle 0.61429 / 0.30 ( 6812) SS BOND : bond 0.00397 / 0.23 ( 9) SS BOND : angle 0.95777 / 0.48 ( 18) hydrogen bonds : bond 0.02912 / 1.83 ( 158) hydrogen bonds : angle 5.19510 / 3.85 ( 450) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 0.95712 / 0.86 ( 3) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 1.44271 / 1.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8454 (mt-10) REVERT: B 465 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: C 105 TYR cc_start: 0.8997 (t80) cc_final: 0.8396 (t80) REVERT: C 220 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6984 (mm-30) REVERT: D 43 GLN cc_start: 0.7502 (mp10) cc_final: 0.6971 (mp10) REVERT: D 82 GLU cc_start: 0.8698 (pm20) cc_final: 0.8345 (pm20) REVERT: D 162 GLU cc_start: 0.8889 (tp30) cc_final: 0.8649 (tp30) REVERT: D 189 LYS cc_start: 0.8889 (pptt) cc_final: 0.8560 (ptmm) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0695 time to fit residues: 6.7787 Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.081380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.060028 restraints weight = 14084.302| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.30 r_work: 0.2821 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5018 Z= 0.136 Angle : 0.627 13.589 6836 Z= 0.304 Chirality : 0.043 0.180 752 Planarity : 0.004 0.048 879 Dihedral : 4.250 22.898 690 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.23 % Allowed : 15.21 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.35), residues: 626 helix: -2.26 (0.68), residues: 39 sheet: 1.06 (0.35), residues: 241 loop : 0.07 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.028 0.001 TYR C 153 PHE 0.007 0.001 PHE D 140 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5007) covalent geometry : angle 0.62537 / 0.30 ( 6812) SS BOND : bond 0.00481 / 0.27 ( 9) SS BOND : angle 0.99458 / 0.54 ( 18) hydrogen bonds : bond 0.02943 / 1.86 ( 158) hydrogen bonds : angle 5.15878 / 3.82 ( 450) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 0.93411 / 0.83 ( 3) link_NAG-ASN : bond 0.00076 / 0.04 ( 1) link_NAG-ASN : angle 1.45694 / 1.00 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.94 seconds wall clock time: 21 minutes 29.90 seconds (1289.90 seconds total)