Starting phenix.real_space_refine on Fri Aug 22 15:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_34742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_34742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_34742.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_34742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgm_34742/08_2025/8hgm_34742.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.42, per 1000 atoms: 0.29 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: 0.52 Conformation dependent library (CDL) restraints added in 223.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 0.79 Time building geometry restraints manager: 0.66 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: 2753 17.76 - 35.51: 207 35.51 - 53.27: 42 53.27 - 71.03: 7 71.03 - 88.78: 3 Dihedral angle restraints: 3012 sinusoidal: 1184 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 3009 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.270 Find NCS groups from input model: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 13.086 88.784 1821 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 aren 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 covalent geometry : bond 0.00355 ( 5007) covalent geometry : angle 0.58837 ( 6812) SS BOND : bond 0.00400 ( 9) SS BOND : angle 0.68148 ( 18) hydrogen bonds : bond 0.27833 ( 158) hydrogen bonds : angle 10.08560 ( 450) link_BETA1-4 : bond 0.00139 ( 1) link_BETA1-4 : angle 1.22620 ( 3) link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 1.72699 ( 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 : 0.146 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: 0.1121 time to fit residues: 11.7671 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 : 0.199 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.081845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060853 restraints weight = 13880.683| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.22 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: 0.8160 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5018 Z= 0.132 Angle : 0.605 13.442 6836 Z= 0.308 Chirality : 0.044 0.170 752 Planarity : 0.004 0.047 879 Dihedral : 4.962 34.842 732 Min Nonbonded Distance : 2.483 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 aren not related in a simple way. whole: 0.16 (0.34), residues: 626 helix: -2.19 (0.67), residues: 39 sheet: 0.89 (0.34), residues: 238 loop : -0.11 (0.34), residues: 349 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 0.008 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 covalent geometry : bond 0.00297 ( 5007) covalent geometry : angle 0.60222 ( 6812) SS BOND : bond 0.00610 ( 9) SS BOND : angle 0.99763 ( 18) hydrogen bonds : bond 0.04439 ( 158) hydrogen bonds : angle 6.77611 ( 450) link_BETA1-4 : bond 0.00042 ( 1) link_BETA1-4 : angle 1.27729 ( 3) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 1.49178 ( 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 : 0.197 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.7158 (t0) cc_final: 0.6493 (t0) REVERT: C 72 MET cc_start: 0.8985 (tpp) cc_final: 0.8765 (mpp) REVERT: C 105 TYR cc_start: 0.8966 (t80) cc_final: 0.8716 (t80) REVERT: D 43 GLN cc_start: 0.7550 (mp10) cc_final: 0.7174 (mp10) REVERT: D 82 GLU cc_start: 0.8732 (pm20) cc_final: 0.8418 (pm20) REVERT: D 139 ASN cc_start: 0.8186 (t0) cc_final: 0.7876 (m-40) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.0929 time to fit residues: 8.0960 Evaluate side-chains 62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3370 r_free = 0.3370 target = 0.081064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.059904 restraints weight = 13979.767| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.23 r_work: 0.2848 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1881 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= 0.145 Angle : 0.597 13.587 6836 Z= 0.297 Chirality : 0.044 0.185 752 Planarity : 0.004 0.048 879 Dihedral : 4.776 34.249 732 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.04 % Allowed : 9.28 % Favored : 88.68 % 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 aren not related in a simple way. whole: 0.23 (0.34), residues: 626 helix: -2.25 (0.66), residues: 39 sheet: 1.05 (0.34), residues: 242 loop : -0.15 (0.35), residues: 345 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 0.014 0.001 PHE C 130 TRP 0.006 0.001 TRP D 149 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5007) covalent geometry : angle 0.59430 ( 6812) SS BOND : bond 0.00434 ( 9) SS BOND : angle 0.92266 ( 18) hydrogen bonds : bond 0.03817 ( 158) hydrogen bonds : angle 6.00248 ( 450) link_BETA1-4 : bond 0.00126 ( 1) link_BETA1-4 : angle 1.30540 ( 3) link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 1.63595 ( 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 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 465 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: B 471 GLU cc_start: 0.8697 (tp30) cc_final: 0.8494 (tp30) REVERT: C 71 ASP cc_start: 0.7137 (t0) cc_final: 0.6519 (t0) REVERT: C 72 MET cc_start: 0.8895 (tpp) cc_final: 0.8652 (mpp) REVERT: C 105 TYR cc_start: 0.8909 (t80) cc_final: 0.8047 (t80) REVERT: C 106 ASP cc_start: 0.9401 (t0) cc_final: 0.9069 (t0) REVERT: D 43 GLN cc_start: 0.7618 (mp10) cc_final: 0.7211 (mp10) REVERT: D 80 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 82 GLU cc_start: 0.8790 (pm20) cc_final: 0.8446 (pm20) REVERT: D 125 GLN cc_start: 0.8301 (tp40) cc_final: 0.7783 (mm-40) REVERT: D 162 GLU cc_start: 0.9118 (tp30) cc_final: 0.8888 (tp30) REVERT: D 189 LYS cc_start: 0.8908 (pptt) cc_final: 0.8659 (ptmm) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.0891 time to fit residues: 7.6400 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP 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 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: 6.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3395 r_free = 0.3395 target = 0.081360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060661 restraints weight = 14031.237| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.14 r_work: 0.2834 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5018 Z= 0.167 Angle : 0.600 14.142 6836 Z= 0.298 Chirality : 0.044 0.179 752 Planarity : 0.004 0.047 879 Dihedral : 4.823 33.974 732 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.78 % Allowed : 10.95 % Favored : 86.27 % 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 aren not related in a simple way. whole: 0.18 (0.35), residues: 626 helix: -2.53 (0.63), residues: 39 sheet: 0.99 (0.34), residues: 243 loop : -0.13 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.023 0.001 TYR C 153 PHE 0.010 0.001 PHE D 140 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5007) covalent geometry : angle 0.59618 ( 6812) SS BOND : bond 0.00531 ( 9) SS BOND : angle 1.08294 ( 18) hydrogen bonds : bond 0.03545 ( 158) hydrogen bonds : angle 5.73580 ( 450) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.36693 ( 3) link_NAG-ASN : bond 0.00367 ( 1) link_NAG-ASN : angle 1.73571 ( 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 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: B 462 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8196 (mtmm) REVERT: B 465 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: B 471 GLU cc_start: 0.8756 (tp30) cc_final: 0.8509 (tp30) REVERT: C 71 ASP cc_start: 0.7172 (t0) cc_final: 0.6592 (t0) REVERT: C 105 TYR cc_start: 0.8897 (t80) cc_final: 0.8074 (t80) REVERT: C 106 ASP cc_start: 0.9470 (t0) cc_final: 0.9131 (t0) REVERT: C 179 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6659 (mm-40) REVERT: D 43 GLN cc_start: 0.7581 (mp10) cc_final: 0.7162 (mp10) REVERT: D 80 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8447 (mm-30) REVERT: D 189 LYS cc_start: 0.8927 (pptt) cc_final: 0.8680 (ptmm) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 0.0935 time to fit residues: 7.9788 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP 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 80 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 44 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061887 restraints weight = 14101.364| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.24 r_work: 0.2859 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5018 Z= 0.103 Angle : 0.569 13.595 6836 Z= 0.280 Chirality : 0.043 0.182 752 Planarity : 0.004 0.047 879 Dihedral : 4.594 32.729 732 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.41 % Allowed : 12.43 % Favored : 85.16 % 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 aren not related in a simple way. whole: 0.34 (0.34), residues: 626 helix: -2.24 (0.71), residues: 33 sheet: 0.99 (0.34), residues: 236 loop : 0.01 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.027 0.001 TYR C 153 PHE 0.006 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 covalent geometry : bond 0.00240 ( 5007) covalent geometry : angle 0.56677 ( 6812) SS BOND : bond 0.00408 ( 9) SS BOND : angle 0.91872 ( 18) hydrogen bonds : bond 0.02987 ( 158) hydrogen bonds : angle 5.49070 ( 450) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.05669 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.39448 ( 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: 13 poor density : 55 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 462 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8209 (mtmm) REVERT: B 465 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: C 71 ASP cc_start: 0.7103 (t0) cc_final: 0.6488 (t0) REVERT: C 105 TYR cc_start: 0.8869 (t80) cc_final: 0.8015 (t80) REVERT: C 106 ASP cc_start: 0.9450 (t0) cc_final: 0.9078 (t0) REVERT: C 179 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6810 (mm-40) REVERT: D 43 GLN cc_start: 0.7501 (mp10) cc_final: 0.6893 (mp10) REVERT: D 189 LYS cc_start: 0.8899 (pptt) cc_final: 0.8641 (ptmm) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0927 time to fit residues: 7.2930 Evaluate side-chains 63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 72 MET 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 170 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060489 restraints weight = 14312.579| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.26 r_work: 0.2830 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5018 Z= 0.163 Angle : 0.593 14.125 6836 Z= 0.293 Chirality : 0.043 0.178 752 Planarity : 0.004 0.047 879 Dihedral : 4.710 33.424 732 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.34 % Allowed : 12.06 % 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 aren not related in a simple way. whole: 0.27 (0.35), residues: 626 helix: -2.57 (0.62), residues: 39 sheet: 1.05 (0.34), residues: 241 loop : -0.06 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.028 0.001 TYR C 153 PHE 0.010 0.001 PHE D 140 TRP 0.005 0.001 TRP B 436 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5007) covalent geometry : angle 0.59004 ( 6812) SS BOND : bond 0.00465 ( 9) SS BOND : angle 0.97344 ( 18) hydrogen bonds : bond 0.03311 ( 158) hydrogen bonds : angle 5.42811 ( 450) link_BETA1-4 : bond 0.00227 ( 1) link_BETA1-4 : angle 1.37069 ( 3) link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 1.70100 ( 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 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8534 (tp30) REVERT: B 462 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8227 (mtmm) REVERT: B 465 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: B 471 GLU cc_start: 0.8782 (tp30) cc_final: 0.8525 (tp30) REVERT: C 105 TYR cc_start: 0.8898 (t80) cc_final: 0.8156 (t80) REVERT: C 106 ASP cc_start: 0.9443 (t0) cc_final: 0.9099 (t0) REVERT: C 179 GLN cc_start: 0.7237 (mm-40) cc_final: 0.7008 (mm-40) REVERT: C 220 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 43 GLN cc_start: 0.7543 (mp10) cc_final: 0.6922 (mp10) outliers start: 18 outliers final: 11 residues processed: 67 average time/residue: 0.0826 time to fit residues: 7.1612 Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.0020 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060148 restraints weight = 14000.273| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.29 r_work: 0.2855 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2629 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= 0.115 Angle : 0.570 13.646 6836 Z= 0.281 Chirality : 0.043 0.174 752 Planarity : 0.004 0.048 879 Dihedral : 4.522 32.371 732 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 13.91 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.41 (0.35), residues: 626 helix: -2.36 (0.69), residues: 33 sheet: 1.03 (0.35), residues: 236 loop : 0.09 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.030 0.001 TYR C 153 PHE 0.006 0.001 PHE C 130 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5007) covalent geometry : angle 0.56819 ( 6812) SS BOND : bond 0.00392 ( 9) SS BOND : angle 0.91010 ( 18) hydrogen bonds : bond 0.02850 ( 158) hydrogen bonds : angle 5.30454 ( 450) link_BETA1-4 : bond 0.00059 ( 1) link_BETA1-4 : angle 1.05115 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.35620 ( 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 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8345 (tp30) REVERT: B 462 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8201 (mtmm) REVERT: B 465 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: B 471 GLU cc_start: 0.8815 (tp30) cc_final: 0.8516 (tp30) REVERT: C 105 TYR cc_start: 0.8930 (t80) cc_final: 0.8222 (t80) REVERT: C 106 ASP cc_start: 0.9444 (t0) cc_final: 0.9082 (t0) REVERT: C 179 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7101 (mm-40) REVERT: C 220 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 43 GLN cc_start: 0.7476 (mp10) cc_final: 0.6889 (mp10) REVERT: D 189 LYS cc_start: 0.8875 (pptt) cc_final: 0.8574 (ptmm) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.0895 time to fit residues: 7.5173 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059060 restraints weight = 14106.542| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.33 r_work: 0.2797 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5018 Z= 0.158 Angle : 0.599 13.951 6836 Z= 0.296 Chirality : 0.044 0.191 752 Planarity : 0.004 0.047 879 Dihedral : 4.616 33.230 732 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.60 % Allowed : 14.66 % Favored : 82.75 % 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 aren not related in a simple way. whole: 0.34 (0.35), residues: 626 helix: -2.54 (0.63), residues: 39 sheet: 1.07 (0.34), residues: 241 loop : 0.02 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.030 0.001 TYR C 153 PHE 0.010 0.001 PHE D 140 TRP 0.008 0.001 TRP D 149 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5007) covalent geometry : angle 0.59679 ( 6812) SS BOND : bond 0.00460 ( 9) SS BOND : angle 0.97090 ( 18) hydrogen bonds : bond 0.03162 ( 158) hydrogen bonds : angle 5.28546 ( 450) link_BETA1-4 : bond 0.00179 ( 1) link_BETA1-4 : angle 1.30778 ( 3) link_NAG-ASN : bond 0.00295 ( 1) link_NAG-ASN : angle 1.63043 ( 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: 14 poor density : 57 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8372 (tp30) REVERT: B 462 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8128 (mtmm) REVERT: B 465 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: C 105 TYR cc_start: 0.8914 (t80) cc_final: 0.8282 (t80) REVERT: C 179 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7097 (mm-40) REVERT: C 220 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 43 GLN cc_start: 0.7445 (mp10) cc_final: 0.6862 (mp10) REVERT: D 159 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7712 (p0) REVERT: D 189 LYS cc_start: 0.8884 (pptt) cc_final: 0.8574 (ptmm) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.0866 time to fit residues: 7.6487 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 159 ASN 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: 5.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060534 restraints weight = 13913.425| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.32 r_work: 0.2858 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5018 Z= 0.111 Angle : 0.588 13.541 6836 Z= 0.290 Chirality : 0.043 0.181 752 Planarity : 0.004 0.049 879 Dihedral : 4.488 32.316 732 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 14.66 % Favored : 82.93 % 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 aren not related in a simple way. whole: 0.37 (0.35), residues: 626 helix: -2.42 (0.63), residues: 39 sheet: 0.98 (0.35), residues: 237 loop : 0.14 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.031 0.001 TYR C 153 PHE 0.006 0.001 PHE C 130 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5007) covalent geometry : angle 0.58606 ( 6812) SS BOND : bond 0.00467 ( 9) SS BOND : angle 0.91817 ( 18) hydrogen bonds : bond 0.02736 ( 158) hydrogen bonds : angle 5.17358 ( 450) link_BETA1-4 : bond 0.00121 ( 1) link_BETA1-4 : angle 0.99413 ( 3) link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.28112 ( 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 79 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8413 (tp30) REVERT: B 462 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8181 (mtmm) REVERT: B 465 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: B 471 GLU cc_start: 0.8771 (tp30) cc_final: 0.8519 (tp30) REVERT: C 105 TYR cc_start: 0.8983 (t80) cc_final: 0.8389 (t80) REVERT: C 179 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7100 (mm-40) REVERT: D 43 GLN cc_start: 0.7425 (mp10) cc_final: 0.6885 (mp10) REVERT: D 82 GLU cc_start: 0.8719 (pm20) cc_final: 0.8381 (pm20) REVERT: D 162 GLU cc_start: 0.8935 (tp30) cc_final: 0.8701 (tp30) REVERT: D 189 LYS cc_start: 0.8870 (pptt) cc_final: 0.8586 (ptmm) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.0900 time to fit residues: 8.5688 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 29 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060811 restraints weight = 14008.995| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.33 r_work: 0.2833 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5018 Z= 0.110 Angle : 0.605 13.419 6836 Z= 0.298 Chirality : 0.043 0.176 752 Planarity : 0.004 0.049 879 Dihedral : 4.386 31.353 732 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.67 % Allowed : 15.58 % Favored : 82.75 % 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 aren not related in a simple way. whole: 0.38 (0.35), residues: 626 helix: -2.39 (0.64), residues: 39 sheet: 1.07 (0.35), residues: 241 loop : 0.05 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.030 0.001 TYR C 153 PHE 0.006 0.001 PHE D 140 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5007) covalent geometry : angle 0.60314 ( 6812) SS BOND : bond 0.00408 ( 9) SS BOND : angle 0.88869 ( 18) hydrogen bonds : bond 0.02638 ( 158) hydrogen bonds : angle 5.11486 ( 450) link_BETA1-4 : bond 0.00113 ( 1) link_BETA1-4 : angle 1.04222 ( 3) link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.29486 ( 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 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8409 (tp30) REVERT: B 462 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8127 (mtmm) REVERT: B 465 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: B 471 GLU cc_start: 0.8805 (tp30) cc_final: 0.8531 (tp30) REVERT: C 105 TYR cc_start: 0.8956 (t80) cc_final: 0.8330 (t80) REVERT: C 179 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7066 (mm-40) REVERT: D 43 GLN cc_start: 0.7322 (mp10) cc_final: 0.6825 (mp10) REVERT: D 189 LYS cc_start: 0.8820 (pptt) cc_final: 0.8519 (ptmm) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.0904 time to fit residues: 7.5011 Evaluate side-chains 63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 57 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060251 restraints weight = 14037.714| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.23 r_work: 0.2856 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2972 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= 0.132 Angle : 0.610 13.458 6836 Z= 0.302 Chirality : 0.043 0.177 752 Planarity : 0.004 0.048 879 Dihedral : 4.450 31.522 732 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.86 % Allowed : 15.96 % Favored : 82.19 % 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 aren not related in a simple way. whole: 0.40 (0.35), residues: 626 helix: -2.50 (0.63), residues: 39 sheet: 1.10 (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 0.030 0.001 TYR C 153 PHE 0.007 0.001 PHE D 140 TRP 0.005 0.001 TRP B 436 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5007) covalent geometry : angle 0.60801 ( 6812) SS BOND : bond 0.00423 ( 9) SS BOND : angle 0.91590 ( 18) hydrogen bonds : bond 0.02867 ( 158) hydrogen bonds : angle 5.10362 ( 450) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 1.17251 ( 3) link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.45252 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.85 seconds wall clock time: 25 minutes 12.59 seconds (1512.59 seconds total)