Starting phenix.real_space_refine on Fri Oct 23 04:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.cif Found real_map, /net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36dk_77401/10_2026/36dk_77401.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 2 5.21 5 S 14 5.16 5 C 5133 2.51 5 N 1361 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8143 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4321 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3060 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 29, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 743 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 17 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3, 'water': 6} Link IDs: {None: 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.97, per 1000 atoms: 0.24 Number of scatterers: 8143 At special positions: 0 Unit cell: (73.659, 105.064, 123.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 38 15.00 Mg 2 11.99 O 1595 8.00 N 1361 7.00 C 5133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 373.6 milliseconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 41.4% alpha, 17.2% beta 14 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.714A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.510A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.507A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.538A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.105A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.539A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 121 through 129 removed outlier: 4.736A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.666A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.695A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.256A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.522A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 470 removed outlier: 6.182A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB2, first strand: chain 'B' and resid 105 through 110 Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.334A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 353 removed outlier: 7.836A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1560 1.33 - 1.45: 2110 1.45 - 1.57: 4651 1.57 - 1.69: 72 1.69 - 1.81: 24 Bond restraints: 8417 Sorted by residual: bond pdb=" C4 DC F 3 " pdb=" N4 DC F 3 " ideal model delta sigma weight residual 1.335 1.296 0.039 9.00e-03 1.23e+04 1.90e+01 bond pdb=" C4 DC F 1 " pdb=" N4 DC F 1 " ideal model delta sigma weight residual 1.335 1.297 0.038 9.00e-03 1.23e+04 1.75e+01 bond pdb=" N3 DC F 3 " pdb=" C4 DC F 3 " ideal model delta sigma weight residual 1.335 1.311 0.024 7.00e-03 2.04e+04 1.18e+01 bond pdb=" N3 DC F 1 " pdb=" C4 DC F 1 " ideal model delta sigma weight residual 1.335 1.313 0.022 7.00e-03 2.04e+04 1.02e+01 bond pdb=" C3' DC F 21 " pdb=" O3' DC F 21 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.01e+01 ... (remaining 8412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10353 1.49 - 2.98: 1024 2.98 - 4.47: 184 4.47 - 5.96: 28 5.96 - 7.45: 4 Bond angle restraints: 11593 Sorted by residual: angle pdb=" O2 DC F 1 " pdb=" C2 DC F 1 " pdb=" N3 DC F 1 " ideal model delta sigma weight residual 121.90 117.32 4.58 7.00e-01 2.04e+00 4.28e+01 angle pdb=" O2 DC F 3 " pdb=" C2 DC F 3 " pdb=" N3 DC F 3 " ideal model delta sigma weight residual 121.90 117.43 4.47 7.00e-01 2.04e+00 4.07e+01 angle pdb=" O4' DG F 32 " pdb=" C1' DG F 32 " pdb=" N9 DG F 32 " ideal model delta sigma weight residual 108.00 112.34 -4.34 7.00e-01 2.04e+00 3.85e+01 angle pdb=" O4' DG F 34 " pdb=" C1' DG F 34 " pdb=" N9 DG F 34 " ideal model delta sigma weight residual 108.00 111.77 -3.77 7.00e-01 2.04e+00 2.90e+01 angle pdb=" O4' DT F 0 " pdb=" C1' DT F 0 " pdb=" N1 DT F 0 " ideal model delta sigma weight residual 108.00 111.70 -3.70 7.00e-01 2.04e+00 2.80e+01 ... (remaining 11588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4421 17.80 - 35.60: 378 35.60 - 53.40: 98 53.40 - 71.20: 37 71.20 - 89.00: 16 Dihedral angle restraints: 4950 sinusoidal: 2302 harmonic: 2648 Sorted by residual: dihedral pdb=" CA ILE B 63 " pdb=" C ILE B 63 " pdb=" N LYS B 64 " pdb=" CA LYS B 64 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ASP A 237 " pdb=" C ASP A 237 " pdb=" N LYS A 238 " pdb=" CA LYS A 238 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA GLN A 464 " pdb=" C GLN A 464 " pdb=" N LYS A 465 " pdb=" CA LYS A 465 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 884 0.064 - 0.127: 311 0.127 - 0.191: 54 0.191 - 0.254: 16 0.254 - 0.318: 8 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C3' DA F 27 " pdb=" C4' DA F 27 " pdb=" O3' DA F 27 " pdb=" C2' DA F 27 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C3' DA F 26 " pdb=" C4' DA F 26 " pdb=" O3' DA F 26 " pdb=" C2' DA F 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' DG F 30 " pdb=" C4' DG F 30 " pdb=" O3' DG F 30 " pdb=" C2' DG F 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1270 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 1 " -0.105 2.00e-02 2.50e+03 5.23e-02 6.16e+01 pdb=" N1 DC F 1 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC F 1 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DC F 1 " 0.043 2.00e-02 2.50e+03 pdb=" N3 DC F 1 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC F 1 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC F 1 " -0.075 2.00e-02 2.50e+03 pdb=" C5 DC F 1 " 0.048 2.00e-02 2.50e+03 pdb=" C6 DC F 1 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' OMC F 2 " -0.076 2.00e-02 2.50e+03 4.07e-02 3.73e+01 pdb=" N1 OMC F 2 " -0.001 2.00e-02 2.50e+03 pdb=" C2 OMC F 2 " 0.005 2.00e-02 2.50e+03 pdb=" O2 OMC F 2 " 0.057 2.00e-02 2.50e+03 pdb=" N3 OMC F 2 " -0.015 2.00e-02 2.50e+03 pdb=" C4 OMC F 2 " -0.022 2.00e-02 2.50e+03 pdb=" N4 OMC F 2 " -0.035 2.00e-02 2.50e+03 pdb=" C5 OMC F 2 " 0.034 2.00e-02 2.50e+03 pdb=" C6 OMC F 2 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' OMC F 4 " -0.059 2.00e-02 2.50e+03 3.35e-02 2.52e+01 pdb=" N1 OMC F 4 " 0.004 2.00e-02 2.50e+03 pdb=" C2 OMC F 4 " -0.006 2.00e-02 2.50e+03 pdb=" O2 OMC F 4 " 0.051 2.00e-02 2.50e+03 pdb=" N3 OMC F 4 " -0.016 2.00e-02 2.50e+03 pdb=" C4 OMC F 4 " -0.029 2.00e-02 2.50e+03 pdb=" N4 OMC F 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 OMC F 4 " 0.022 2.00e-02 2.50e+03 pdb=" C6 OMC F 4 " 0.047 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 7 2.36 - 3.00: 4048 3.00 - 3.63: 12420 3.63 - 4.27: 20477 4.27 - 4.90: 32126 Nonbonded interactions: 69078 Sorted by model distance: nonbonded pdb=" O6 POP A 601 " pdb="MG MG A 602 " model vdw 1.729 2.170 nonbonded pdb=" O VAL A 111 " pdb="MG MG A 602 " model vdw 1.795 2.170 nonbonded pdb=" OD2 ASP A 185 " pdb="MG MG A 602 " model vdw 1.852 2.170 nonbonded pdb=" OP1 DA F 35 " pdb="MG MG A 603 " model vdw 1.865 2.170 nonbonded pdb=" OD1 ASP A 110 " pdb="MG MG A 603 " model vdw 1.876 2.170 ... (remaining 69073 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: 20.910 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.470 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8417 Z= 0.398 Angle : 0.970 7.452 11593 Z= 0.623 Chirality : 0.070 0.318 1273 Planarity : 0.009 0.144 1332 Dihedral : 15.903 89.000 3238 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.34 % Favored : 98.54 % Rotamer: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.18 (0.25), residues: 893 helix: 0.33 (0.26), residues: 320 sheet: -0.00 (0.35), residues: 167 loop : -0.40 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 78 TYR 0.044 0.008 TYR A 342 PHE 0.023 0.004 PHE A 389 TRP 0.031 0.006 TRP A 426 HIS 0.015 0.003 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.40 ( 8417) covalent geometry : angle 0.96981 / 0.62 (11593) hydrogen bonds : bond 0.14409 / 9.56 ( 375) hydrogen bonds : angle 6.17043 / 4.09 ( 979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8478 (mmtm) REVERT: A 344 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8279 (mm-30) REVERT: A 415 GLU cc_start: 0.8396 (tt0) cc_final: 0.8037 (mp0) REVERT: A 448 ARG cc_start: 0.6497 (mtm180) cc_final: 0.5349 (mtt180) REVERT: B 11 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7867 (pptt) REVERT: B 278 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8342 (mm-40) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.7223 time to fit residues: 80.9749 Evaluate side-chains 74 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS A 373 GLN A 520 GLN B 147 ASN B 394 GLN B 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086905 restraints weight = 11877.905| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.93 r_work: 0.3142 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8417 Z= 0.189 Angle : 0.629 7.497 11593 Z= 0.346 Chirality : 0.046 0.223 1273 Planarity : 0.004 0.032 1332 Dihedral : 15.027 59.656 1339 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.11 % Allowed : 5.56 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 893 helix: 2.32 (0.29), residues: 308 sheet: 0.39 (0.37), residues: 163 loop : 0.01 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 307 TYR 0.014 0.002 TYR A 144 PHE 0.020 0.002 PHE A 160 TRP 0.019 0.002 TRP A 88 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 8417) covalent geometry : angle 0.62879 / 0.35 (11593) hydrogen bonds : bond 0.04910 / 3.22 ( 375) hydrogen bonds : angle 4.89756 / 3.29 ( 979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.271 Fit side-chains REVERT: A 22 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6760 (tptp) REVERT: A 311 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8533 (mmtm) REVERT: A 404 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: A 415 GLU cc_start: 0.8456 (tt0) cc_final: 0.8167 (mp0) REVERT: A 448 ARG cc_start: 0.6671 (mtm180) cc_final: 0.5764 (mtt180) REVERT: B 11 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7982 (pptt) REVERT: B 277 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7832 (ptm160) REVERT: B 281 LYS cc_start: 0.8556 (mttp) cc_final: 0.8293 (mmtm) outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 0.7858 time to fit residues: 65.8092 Evaluate side-chains 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [38, 4, 25, 67, 37, 33, 30, 10, 58, 14, 68] chunk 38 optimal weight: 0.0000 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086744 restraints weight = 11686.820| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.97 r_work: 0.3087 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8417 Z= 0.157 Angle : 0.569 5.920 11593 Z= 0.313 Chirality : 0.044 0.204 1273 Planarity : 0.004 0.028 1332 Dihedral : 15.075 59.889 1339 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.99 % Allowed : 6.54 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.28), residues: 893 helix: 2.65 (0.29), residues: 308 sheet: 0.43 (0.37), residues: 163 loop : 0.13 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.011 0.001 TYR A 144 PHE 0.018 0.002 PHE A 160 TRP 0.015 0.001 TRP A 88 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 8417) covalent geometry : angle 0.56925 / 0.31 (11593) hydrogen bonds : bond 0.04399 / 2.88 ( 375) hydrogen bonds : angle 4.60601 / 3.08 ( 979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.337 Fit side-chains REVERT: A 22 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6761 (tptp) REVERT: A 311 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8486 (mmtm) REVERT: A 404 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 415 GLU cc_start: 0.8469 (tt0) cc_final: 0.8023 (mp0) REVERT: A 431 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8670 (mmtt) REVERT: A 448 ARG cc_start: 0.6711 (mtm180) cc_final: 0.5751 (mtt180) REVERT: B 11 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8059 (pptt) REVERT: B 277 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.8013 (mmm-85) REVERT: B 281 LYS cc_start: 0.8545 (mttp) cc_final: 0.8325 (mmtm) outliers start: 8 outliers final: 1 residues processed: 83 average time/residue: 0.7709 time to fit residues: 66.9764 Evaluate side-chains 73 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [59, 70, 76, 41, 12, 45, 82, 4, 58, 47, 37] chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087587 restraints weight = 11962.367| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.95 r_work: 0.3137 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8417 Z= 0.158 Angle : 0.551 5.831 11593 Z= 0.302 Chirality : 0.044 0.199 1273 Planarity : 0.004 0.031 1332 Dihedral : 15.119 59.572 1339 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.11 % Allowed : 7.41 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.28), residues: 893 helix: 2.72 (0.29), residues: 308 sheet: 0.43 (0.37), residues: 163 loop : 0.11 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.011 0.001 TYR A 144 PHE 0.018 0.002 PHE A 160 TRP 0.014 0.001 TRP A 88 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 8417) covalent geometry : angle 0.55084 / 0.30 (11593) hydrogen bonds : bond 0.04182 / 2.74 ( 375) hydrogen bonds : angle 4.49932 / 3.00 ( 979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.284 Fit side-chains REVERT: A 22 LYS cc_start: 0.7332 (mmmt) cc_final: 0.6855 (tptp) REVERT: A 311 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8543 (mmtm) REVERT: A 404 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 415 GLU cc_start: 0.8459 (tt0) cc_final: 0.8118 (mp0) REVERT: A 431 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8706 (mmtt) REVERT: A 448 ARG cc_start: 0.6754 (mtm180) cc_final: 0.5796 (mmt180) REVERT: B 11 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8150 (pptt) REVERT: B 69 THR cc_start: 0.8723 (p) cc_final: 0.8508 (t) REVERT: B 199 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7705 (mpt180) REVERT: B 277 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.8031 (mmm-85) REVERT: B 281 LYS cc_start: 0.8607 (mttp) cc_final: 0.8399 (mmtm) outliers start: 9 outliers final: 1 residues processed: 81 average time/residue: 0.7903 time to fit residues: 67.0204 Evaluate side-chains 77 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [86, 68, 77, 17, 43, 40, 70, 33, 37, 65, 75] chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086979 restraints weight = 11713.786| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.95 r_work: 0.3106 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8417 Z= 0.157 Angle : 0.549 5.785 11593 Z= 0.300 Chirality : 0.044 0.197 1273 Planarity : 0.004 0.033 1332 Dihedral : 15.155 59.848 1339 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.74 % Allowed : 8.15 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 893 helix: 2.72 (0.29), residues: 309 sheet: 0.36 (0.37), residues: 166 loop : 0.12 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.011 0.001 TYR A 188 PHE 0.017 0.002 PHE A 160 TRP 0.014 0.001 TRP A 88 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 8417) covalent geometry : angle 0.54886 / 0.30 (11593) hydrogen bonds : bond 0.04064 / 2.66 ( 375) hydrogen bonds : angle 4.41600 / 2.93 ( 979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.321 Fit side-chains REVERT: A 22 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6845 (tptp) REVERT: A 311 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8491 (mmtm) REVERT: A 404 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: A 415 GLU cc_start: 0.8472 (tt0) cc_final: 0.8040 (mp0) REVERT: A 431 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8666 (mmtt) REVERT: A 448 ARG cc_start: 0.6832 (mtm180) cc_final: 0.5868 (mmt180) REVERT: B 11 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8131 (pptt) REVERT: B 69 THR cc_start: 0.8724 (p) cc_final: 0.8509 (t) REVERT: B 199 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7653 (mpt180) REVERT: B 277 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.8013 (mmm-85) REVERT: B 281 LYS cc_start: 0.8591 (mttp) cc_final: 0.8353 (mmtm) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 0.7839 time to fit residues: 60.8205 Evaluate side-chains 70 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [51, 30, 19, 4, 9, 74, 43, 14, 32, 27, 28] chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089519 restraints weight = 11735.145| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.93 r_work: 0.3138 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8417 Z= 0.117 Angle : 0.500 5.927 11593 Z= 0.274 Chirality : 0.042 0.182 1273 Planarity : 0.003 0.035 1332 Dihedral : 15.057 59.617 1339 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.11 % Allowed : 8.89 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.28), residues: 893 helix: 2.86 (0.29), residues: 309 sheet: 0.50 (0.37), residues: 165 loop : 0.16 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.009 0.001 TYR A 188 PHE 0.011 0.001 PHE A 160 TRP 0.012 0.001 TRP A 402 HIS 0.001 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 8417) covalent geometry : angle 0.49985 / 0.27 (11593) hydrogen bonds : bond 0.03440 / 2.23 ( 375) hydrogen bonds : angle 4.26329 / 2.82 ( 979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.353 Fit side-chains REVERT: A 22 LYS cc_start: 0.7358 (mmmt) cc_final: 0.6835 (tptp) REVERT: A 237 ASP cc_start: 0.8450 (p0) cc_final: 0.8152 (m-30) REVERT: A 311 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8479 (mmtm) REVERT: A 404 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: A 415 GLU cc_start: 0.8419 (tt0) cc_final: 0.8010 (mp0) REVERT: A 431 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8613 (mmtt) REVERT: A 448 ARG cc_start: 0.6864 (mtm180) cc_final: 0.5922 (mmt180) REVERT: B 11 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8138 (pptt) REVERT: B 69 THR cc_start: 0.8710 (p) cc_final: 0.8506 (t) REVERT: B 199 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7645 (mpt180) REVERT: B 277 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: B 281 LYS cc_start: 0.8588 (mttp) cc_final: 0.8340 (mmtm) outliers start: 9 outliers final: 1 residues processed: 78 average time/residue: 0.7725 time to fit residues: 63.2704 Evaluate side-chains 73 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [43, 5, 29, 15, 12, 90, 37, 1, 55, 48, 27] chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085063 restraints weight = 11844.371| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.96 r_work: 0.3067 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8417 Z= 0.256 Angle : 0.626 7.548 11593 Z= 0.337 Chirality : 0.048 0.279 1273 Planarity : 0.004 0.043 1332 Dihedral : 15.375 59.810 1339 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.60 % Allowed : 8.64 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.28), residues: 893 helix: 2.61 (0.29), residues: 309 sheet: 0.30 (0.36), residues: 172 loop : 0.15 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.013 0.002 TYR A 144 PHE 0.026 0.002 PHE A 160 TRP 0.016 0.002 TRP A 88 HIS 0.006 0.002 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 ( 8417) covalent geometry : angle 0.62618 / 0.34 (11593) hydrogen bonds : bond 0.04972 / 3.30 ( 375) hydrogen bonds : angle 4.53352 / 3.01 ( 979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.7506 (mmmt) cc_final: 0.6933 (tptp) REVERT: A 311 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8500 (mmtm) REVERT: A 404 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: A 415 GLU cc_start: 0.8554 (tt0) cc_final: 0.8113 (mp0) REVERT: A 431 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8653 (mmtt) REVERT: A 448 ARG cc_start: 0.6933 (mtm180) cc_final: 0.6006 (mtt90) REVERT: B 11 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8133 (pptt) REVERT: B 69 THR cc_start: 0.8727 (p) cc_final: 0.8507 (t) REVERT: B 281 LYS cc_start: 0.8593 (mttp) cc_final: 0.8341 (mmtm) outliers start: 13 outliers final: 4 residues processed: 74 average time/residue: 0.7718 time to fit residues: 59.8165 Evaluate side-chains 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 275 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [61, 38, 75, 85, 5, 42, 82, 68, 53, 46, 18] chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN B 278 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.112992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087293 restraints weight = 11714.222| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.94 r_work: 0.3114 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8417 Z= 0.141 Angle : 0.539 6.621 11593 Z= 0.293 Chirality : 0.043 0.195 1273 Planarity : 0.004 0.041 1332 Dihedral : 15.299 59.953 1339 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.99 % Allowed : 9.26 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.28), residues: 893 helix: 2.72 (0.29), residues: 309 sheet: 0.26 (0.36), residues: 176 loop : 0.13 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 277 TYR 0.011 0.001 TYR A 188 PHE 0.015 0.001 PHE A 160 TRP 0.014 0.001 TRP A 88 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8417) covalent geometry : angle 0.53935 / 0.29 (11593) hydrogen bonds : bond 0.03863 / 2.52 ( 375) hydrogen bonds : angle 4.36039 / 2.90 ( 979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.339 Fit side-chains REVERT: A 22 LYS cc_start: 0.7467 (mmmt) cc_final: 0.6905 (tptp) REVERT: A 41 MET cc_start: 0.8212 (mtp) cc_final: 0.7975 (mtm) REVERT: A 237 ASP cc_start: 0.8481 (p0) cc_final: 0.8125 (m-30) REVERT: A 311 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8494 (mmtm) REVERT: A 404 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 415 GLU cc_start: 0.8464 (tt0) cc_final: 0.8032 (mp0) REVERT: A 431 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8630 (mmtt) REVERT: A 448 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6031 (mtt90) REVERT: B 11 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8138 (pptt) REVERT: B 69 THR cc_start: 0.8733 (p) cc_final: 0.8519 (t) REVERT: B 281 LYS cc_start: 0.8585 (mttp) cc_final: 0.8366 (mmtm) outliers start: 8 outliers final: 2 residues processed: 69 average time/residue: 0.7996 time to fit residues: 57.8802 Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 275 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [27, 20, 50, 24, 29, 84, 66, 73, 88, 13, 2] chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087852 restraints weight = 11741.084| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.95 r_work: 0.3124 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8417 Z= 0.136 Angle : 0.528 7.451 11593 Z= 0.287 Chirality : 0.043 0.193 1273 Planarity : 0.004 0.035 1332 Dihedral : 15.135 59.788 1339 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.62 % Allowed : 9.75 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.28), residues: 893 helix: 2.76 (0.29), residues: 309 sheet: 0.32 (0.36), residues: 175 loop : 0.13 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 277 TYR 0.010 0.001 TYR A 188 PHE 0.015 0.001 PHE A 160 TRP 0.013 0.001 TRP A 88 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 8417) covalent geometry : angle 0.52812 / 0.29 (11593) hydrogen bonds : bond 0.03733 / 2.44 ( 375) hydrogen bonds : angle 4.30409 / 2.85 ( 979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.426 Fit side-chains REVERT: A 22 LYS cc_start: 0.7485 (mmmt) cc_final: 0.6922 (tptp) REVERT: A 237 ASP cc_start: 0.8475 (p0) cc_final: 0.8141 (m-30) REVERT: A 311 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8493 (mmtm) REVERT: A 404 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 415 GLU cc_start: 0.8440 (tt0) cc_final: 0.8018 (mp0) REVERT: A 431 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8628 (mmtt) REVERT: A 448 ARG cc_start: 0.7045 (mtm180) cc_final: 0.5995 (mtt180) REVERT: B 11 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8132 (pptt) REVERT: B 69 THR cc_start: 0.8731 (p) cc_final: 0.8518 (t) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.8124 time to fit residues: 62.9978 Evaluate side-chains 70 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 275 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [20, 52, 1, 78, 31, 79, 6, 53, 37, 84, 56] chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087853 restraints weight = 11763.830| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.95 r_work: 0.3121 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8417 Z= 0.141 Angle : 0.533 7.843 11593 Z= 0.290 Chirality : 0.043 0.192 1273 Planarity : 0.004 0.035 1332 Dihedral : 15.124 59.389 1339 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.49 % Allowed : 10.49 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.28), residues: 893 helix: 2.74 (0.29), residues: 309 sheet: 0.30 (0.36), residues: 175 loop : 0.16 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.010 0.001 TYR A 188 PHE 0.016 0.001 PHE A 160 TRP 0.013 0.001 TRP A 88 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8417) covalent geometry : angle 0.53326 / 0.29 (11593) hydrogen bonds : bond 0.03772 / 2.47 ( 375) hydrogen bonds : angle 4.31029 / 2.86 ( 979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.250 Fit side-chains REVERT: A 22 LYS cc_start: 0.7463 (mmmt) cc_final: 0.6889 (tptp) REVERT: A 41 MET cc_start: 0.8172 (mtp) cc_final: 0.7856 (mtm) REVERT: A 237 ASP cc_start: 0.8478 (p0) cc_final: 0.8109 (m-30) REVERT: A 311 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8481 (mmtm) REVERT: A 404 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: A 415 GLU cc_start: 0.8444 (tt0) cc_final: 0.8009 (mp0) REVERT: A 431 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8627 (mmtt) REVERT: A 448 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6274 (ttt180) REVERT: B 11 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8116 (pptt) REVERT: B 69 THR cc_start: 0.8709 (p) cc_final: 0.8492 (t) REVERT: B 242 GLN cc_start: 0.6601 (tp-100) cc_final: 0.6118 (tm130) REVERT: B 277 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7661 (mmm-85) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.8029 time to fit residues: 62.9205 Evaluate side-chains 70 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 275 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [2, 52, 22, 32, 31, 58, 13, 42, 26, 34, 55] chunk 2 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 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 = 0.3681 r_free = 0.3681 target = 0.113489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087931 restraints weight = 11805.375| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.95 r_work: 0.3126 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8417 Z= 0.140 Angle : 0.538 9.211 11593 Z= 0.292 Chirality : 0.043 0.190 1273 Planarity : 0.004 0.035 1332 Dihedral : 15.118 59.361 1339 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.74 % Allowed : 10.25 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 893 helix: 2.76 (0.29), residues: 309 sheet: 0.29 (0.36), residues: 175 loop : 0.17 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 277 TYR 0.010 0.001 TYR A 188 PHE 0.015 0.001 PHE A 160 TRP 0.013 0.001 TRP A 88 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8417) covalent geometry : angle 0.53789 / 0.29 (11593) hydrogen bonds : bond 0.03717 / 2.43 ( 375) hydrogen bonds : angle 4.29485 / 2.85 ( 979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.96 seconds wall clock time: 66 minutes 54.03 seconds (4014.03 seconds total)