Starting phenix.real_space_refine on Fri Oct 23 05:42:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kjv_22899/10_2026/7kjv_22899.cif" } resolution = 2.8 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= 0.086 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 44 5.49 5 Mg 1 5.21 5 S 12 5.16 5 C 5250 2.51 5 N 1410 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4186 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 18, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3214 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 30, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNAv2': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Unusual residues: {'G47': 1} Classifications: {'DNA_mixed': 1, 'RNAv2': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MG': 1, 'BOG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.81, per 1000 atoms: 0.22 Number of scatterers: 8361 At special positions: 0 Unit cell: (77.08, 101.68, 117.26, 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 12 16.00 P 44 15.00 Mg 1 11.99 O 1644 8.00 N 1410 7.00 C 5250 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 214.7 milliseconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 40.8% alpha, 14.6% beta 21 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.352A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.786A 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 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' 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: 3.676A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.723A pdb=" N GLN A 222 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.429A 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 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.941A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 91 removed outlier: 5.107A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.568A pdb=" N PHE B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.633A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.869A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.937A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 4.051A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 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 helix chain 'B' and resid 422 through 427 removed outlier: 3.548A pdb=" N LEU B 425 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) 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 61 removed outlier: 3.560A pdb=" N PHE A 61 " --> pdb=" O LEU A 74 " (cutoff:3.500A) 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 347 through 354 removed outlier: 8.298A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.626A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 468 removed outlier: 4.031A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 355 removed outlier: 6.051A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2425 1.34 - 1.46: 1736 1.46 - 1.58: 4403 1.58 - 1.69: 86 1.69 - 1.81: 21 Bond restraints: 8671 Sorted by residual: bond pdb=" P G47 D 71 " pdb=" O5' G47 D 71 " ideal model delta sigma weight residual 1.684 1.588 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3' G47 D 71 " pdb=" P C D 72 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" CA ARG B 277 " pdb=" C ARG B 277 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.26e-02 6.30e+03 7.65e+00 bond pdb=" C1 BOG A 702 " pdb=" O1 BOG A 702 " ideal model delta sigma weight residual 1.372 1.426 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CA GLN B 394 " pdb=" C GLN B 394 " ideal model delta sigma weight residual 1.524 1.555 -0.032 1.26e-02 6.30e+03 6.39e+00 ... (remaining 8666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 11749 1.70 - 3.40: 239 3.40 - 5.09: 26 5.09 - 6.79: 3 6.79 - 8.49: 3 Bond angle restraints: 12020 Sorted by residual: angle pdb=" N LYS B 395 " pdb=" CA LYS B 395 " pdb=" C LYS B 395 " ideal model delta sigma weight residual 111.28 115.38 -4.10 1.09e+00 8.42e-01 1.42e+01 angle pdb=" O ILE B 393 " pdb=" C ILE B 393 " pdb=" N GLN B 394 " ideal model delta sigma weight residual 123.00 119.00 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" C THR B 107 " pdb=" CA THR B 107 " pdb=" CB THR B 107 " ideal model delta sigma weight residual 109.50 115.41 -5.91 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C6A G47 D 71 " pdb=" C7A G47 D 71 " pdb=" SG G47 D 71 " ideal model delta sigma weight residual 114.07 105.58 8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" O VAL B 276 " pdb=" C VAL B 276 " pdb=" N ARG B 277 " ideal model delta sigma weight residual 122.57 119.37 3.20 1.25e+00 6.40e-01 6.54e+00 ... (remaining 12015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4516 17.28 - 34.56: 412 34.56 - 51.84: 95 51.84 - 69.12: 33 69.12 - 86.40: 16 Dihedral angle restraints: 5072 sinusoidal: 2326 harmonic: 2746 Sorted by residual: dihedral pdb=" O5' G D 70 " pdb=" C5' G D 70 " pdb=" C4' G D 70 " pdb=" C3' G D 70 " ideal model delta sinusoidal sigma weight residual 180.00 152.21 27.79 3 6.40e+00 2.44e-02 2.30e+01 dihedral pdb=" O5' G D 69 " pdb=" C5' G D 69 " pdb=" C4' G D 69 " pdb=" C3' G D 69 " ideal model delta sinusoidal sigma weight residual 60.00 33.72 26.28 3 6.40e+00 2.44e-02 2.10e+01 dihedral pdb=" CA VAL A 552 " pdb=" C VAL A 552 " pdb=" N SER A 553 " pdb=" CA SER A 553 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1111 0.050 - 0.100: 160 0.100 - 0.150: 57 0.150 - 0.200: 4 0.200 - 0.251: 43 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C3' G47 D 71 " pdb=" C4' G47 D 71 " pdb=" O3' G47 D 71 " pdb=" C2' G47 D 71 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" P G D 70 " pdb=" OP1 G D 70 " pdb=" OP2 G D 70 " pdb=" O5' G D 70 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" P G C 183 " pdb=" OP1 G C 183 " pdb=" OP2 G C 183 " pdb=" O5' G C 183 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1372 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.074 2.00e-02 2.50e+03 1.40e-01 6.38e+02 pdb=" N9 G47 D 71 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.069 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.094 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.027 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.063 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.070 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.131 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.206 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.121 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.042 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 393 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ILE B 393 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE B 393 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN B 394 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 271 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO B 272 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.035 5.00e-02 4.00e+02 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1284 2.76 - 3.30: 8083 3.30 - 3.83: 15109 3.83 - 4.37: 18018 4.37 - 4.90: 29489 Nonbonded interactions: 71983 Sorted by model distance: nonbonded pdb=" NE ARG A 557 " pdb=" OP1 U C 201 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU A 122 " pdb=" NH1 ARG A 125 " model vdw 2.228 3.120 nonbonded pdb=" O GLY A 444 " pdb=" NE2 GLN A 478 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS B 82 " pdb=" OE2 GLU B 413 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR A 354 " pdb=" OE1 GLU A 370 " model vdw 2.262 3.040 ... (remaining 71978 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.690 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.003 0.096 8672 Z= 0.153 Angle : 0.554 8.489 12020 Z= 0.269 Chirality : 0.058 0.251 1375 Planarity : 0.005 0.140 1351 Dihedral : 15.028 86.402 3300 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.67 (0.29), residues: 929 helix: 1.95 (0.30), residues: 335 sheet: -0.04 (0.43), residues: 156 loop : -0.53 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 72 TYR 0.016 0.001 TYR A 483 PHE 0.013 0.001 PHE A 346 TRP 0.012 0.001 TRP B 410 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 8671) covalent geometry : angle 0.55409 / 0.27 (12020) hydrogen bonds : bond 0.15712 / 11.05 ( 390) hydrogen bonds : angle 6.55633 / 4.75 ( 1037) Misc. bond : bond 0.03848 / 2.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.304 Fit side-chains REVERT: A 323 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7594 (mtmm) REVERT: A 431 LYS cc_start: 0.8536 (mttp) cc_final: 0.8085 (mptt) REVERT: A 511 ASP cc_start: 0.7021 (m-30) cc_final: 0.6795 (m-30) REVERT: B 28 GLU cc_start: 0.7582 (tp30) cc_final: 0.7188 (tm-30) REVERT: B 40 GLU cc_start: 0.7361 (tp30) cc_final: 0.6732 (pt0) REVERT: B 234 LEU cc_start: 0.7995 (mt) cc_final: 0.7784 (mt) REVERT: B 294 PRO cc_start: 0.8789 (Cg_endo) cc_final: 0.8392 (Cg_exo) REVERT: B 394 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7243 (tt0) REVERT: B 395 LYS cc_start: 0.8471 (tttt) cc_final: 0.8248 (tttp) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.5700 time to fit residues: 64.8453 Evaluate side-chains 67 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 242 GLN A 487 GLN B 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112508 restraints weight = 9301.393| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.56 r_work: 0.3210 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8672 Z= 0.284 Angle : 0.688 10.332 12020 Z= 0.333 Chirality : 0.050 0.225 1375 Planarity : 0.005 0.057 1351 Dihedral : 11.225 70.696 1539 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.23 % Allowed : 9.07 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.26 (0.28), residues: 929 helix: 1.45 (0.29), residues: 333 sheet: -0.35 (0.42), residues: 157 loop : -0.57 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 72 TYR 0.014 0.002 TYR A 188 PHE 0.017 0.002 PHE B 416 TRP 0.017 0.002 TRP B 88 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.28 ( 8671) covalent geometry : angle 0.68792 / 0.33 (12020) hydrogen bonds : bond 0.04321 / 2.98 ( 390) hydrogen bonds : angle 5.46812 / 3.98 ( 1037) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.316 Fit side-chains REVERT: A 41 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5475 (mtt) REVERT: A 110 ASP cc_start: 0.7558 (p0) cc_final: 0.7147 (t0) REVERT: A 347 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7761 (mtmt) REVERT: A 356 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.6932 (mpp-170) REVERT: A 431 LYS cc_start: 0.8985 (mttp) cc_final: 0.8266 (mptt) REVERT: A 511 ASP cc_start: 0.7367 (m-30) cc_final: 0.7117 (m-30) REVERT: A 549 ASP cc_start: 0.8037 (t70) cc_final: 0.7703 (t0) REVERT: B 28 GLU cc_start: 0.8289 (tp30) cc_final: 0.7907 (tm-30) REVERT: B 40 GLU cc_start: 0.8118 (tp30) cc_final: 0.6901 (pt0) REVERT: B 294 PRO cc_start: 0.8740 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: B 328 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: B 388 LYS cc_start: 0.8815 (tttp) cc_final: 0.8609 (tmtp) REVERT: B 395 LYS cc_start: 0.8680 (tttt) cc_final: 0.8411 (tttt) REVERT: B 407 GLN cc_start: 0.8989 (mt0) cc_final: 0.8583 (mm-40) outliers start: 17 outliers final: 7 residues processed: 80 average time/residue: 0.5164 time to fit residues: 44.3755 Evaluate side-chains 68 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [19, 82, 28, 63, 68, 23, 7, 58, 67, 95, 61] chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120357 restraints weight = 9277.288| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.55 r_work: 0.3299 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8672 Z= 0.137 Angle : 0.568 7.580 12020 Z= 0.272 Chirality : 0.045 0.180 1375 Planarity : 0.004 0.051 1351 Dihedral : 10.889 70.690 1539 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.10 % Allowed : 11.70 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.47 (0.28), residues: 929 helix: 1.81 (0.29), residues: 334 sheet: -0.53 (0.41), residues: 158 loop : -0.49 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 72 TYR 0.011 0.001 TYR A 188 PHE 0.013 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8671) covalent geometry : angle 0.56849 / 0.27 (12020) hydrogen bonds : bond 0.03508 / 2.40 ( 390) hydrogen bonds : angle 5.11134 / 3.73 ( 1037) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.318 Fit side-chains REVERT: A 41 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5873 (mtt) REVERT: A 110 ASP cc_start: 0.7565 (p0) cc_final: 0.7246 (t0) REVERT: A 356 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.7066 (mpt180) REVERT: A 358 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7640 (ttm170) REVERT: A 431 LYS cc_start: 0.9082 (mttp) cc_final: 0.8526 (mptt) REVERT: A 549 ASP cc_start: 0.8047 (t70) cc_final: 0.7821 (t0) REVERT: B 28 GLU cc_start: 0.8277 (tp30) cc_final: 0.7983 (tm-30) REVERT: B 294 PRO cc_start: 0.8957 (Cg_endo) cc_final: 0.8528 (Cg_exo) REVERT: B 328 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8439 (tt0) outliers start: 16 outliers final: 5 residues processed: 82 average time/residue: 0.4898 time to fit residues: 43.2142 Evaluate side-chains 65 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [79, 3, 19, 38, 89, 7, 31, 66, 76, 0, 86] chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.159910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120843 restraints weight = 9420.028| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.55 r_work: 0.3309 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8672 Z= 0.142 Angle : 0.567 10.712 12020 Z= 0.267 Chirality : 0.045 0.178 1375 Planarity : 0.004 0.047 1351 Dihedral : 10.822 70.225 1539 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.37 % Allowed : 13.27 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.49 (0.28), residues: 929 helix: 1.82 (0.29), residues: 334 sheet: -0.75 (0.40), residues: 169 loop : -0.36 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.011 0.001 TYR A 183 PHE 0.021 0.001 PHE A 130 TRP 0.015 0.001 TRP B 88 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8671) covalent geometry : angle 0.56692 / 0.27 (12020) hydrogen bonds : bond 0.03332 / 2.28 ( 390) hydrogen bonds : angle 4.96290 / 3.62 ( 1037) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.302 Fit side-chains REVERT: A 41 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5530 (mtt) REVERT: A 110 ASP cc_start: 0.7506 (p0) cc_final: 0.7042 (t0) REVERT: A 323 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7695 (mtmm) REVERT: A 356 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.6721 (mpt180) REVERT: A 358 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: A 388 LYS cc_start: 0.8091 (mttm) cc_final: 0.7436 (tptt) REVERT: A 431 LYS cc_start: 0.9047 (mttp) cc_final: 0.8511 (mptt) REVERT: A 549 ASP cc_start: 0.7930 (t70) cc_final: 0.7617 (t0) REVERT: B 328 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: B 407 GLN cc_start: 0.8937 (mt0) cc_final: 0.8608 (mm-40) outliers start: 18 outliers final: 6 residues processed: 78 average time/residue: 0.5208 time to fit residues: 43.6096 Evaluate side-chains 69 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [48, 94, 73, 75, 58, 0, 81, 72, 24, 31, 66] chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN B 91 GLN B 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120395 restraints weight = 9453.599| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.56 r_work: 0.3308 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8672 Z= 0.139 Angle : 0.557 8.689 12020 Z= 0.263 Chirality : 0.044 0.180 1375 Planarity : 0.004 0.043 1351 Dihedral : 10.838 70.034 1539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 14.06 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.54 (0.28), residues: 929 helix: 1.87 (0.29), residues: 334 sheet: -0.80 (0.39), residues: 174 loop : -0.29 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 72 TYR 0.012 0.001 TYR A 183 PHE 0.011 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8671) covalent geometry : angle 0.55696 / 0.26 (12020) hydrogen bonds : bond 0.03269 / 2.22 ( 390) hydrogen bonds : angle 4.89894 / 3.58 ( 1037) Misc. bond : bond 0.00024 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.198 Fit side-chains REVERT: A 41 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5506 (mtt) REVERT: A 110 ASP cc_start: 0.7428 (p0) cc_final: 0.6990 (t0) REVERT: A 323 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7710 (mtmm) REVERT: A 356 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.6664 (mpt180) REVERT: A 358 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7568 (ttm170) REVERT: A 388 LYS cc_start: 0.8131 (mttm) cc_final: 0.7439 (tptt) REVERT: A 431 LYS cc_start: 0.9035 (mttp) cc_final: 0.8477 (mptt) REVERT: A 549 ASP cc_start: 0.7876 (t70) cc_final: 0.7570 (t0) REVERT: B 328 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: B 407 GLN cc_start: 0.8943 (mt0) cc_final: 0.8619 (mm-40) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.4639 time to fit residues: 36.0369 Evaluate side-chains 69 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [63, 26, 67, 22, 95, 62, 9, 84, 61, 5, 40] chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121828 restraints weight = 9331.004| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.54 r_work: 0.3325 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8672 Z= 0.121 Angle : 0.541 7.793 12020 Z= 0.255 Chirality : 0.044 0.181 1375 Planarity : 0.004 0.040 1351 Dihedral : 10.647 70.417 1539 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.58 % Allowed : 15.37 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.59 (0.28), residues: 929 helix: 1.94 (0.29), residues: 336 sheet: -0.83 (0.38), residues: 178 loop : -0.26 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.010 0.001 TYR A 188 PHE 0.010 0.001 PHE B 416 TRP 0.016 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8671) covalent geometry : angle 0.54083 / 0.25 (12020) hydrogen bonds : bond 0.03115 / 2.11 ( 390) hydrogen bonds : angle 4.81289 / 3.51 ( 1037) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.306 Fit side-chains REVERT: A 41 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5638 (mtt) REVERT: A 110 ASP cc_start: 0.7385 (p0) cc_final: 0.7013 (t0) REVERT: A 323 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7744 (mtmm) REVERT: A 356 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.6835 (mpp-170) REVERT: A 358 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: A 388 LYS cc_start: 0.8123 (mttm) cc_final: 0.7488 (tptt) REVERT: A 431 LYS cc_start: 0.9027 (mttp) cc_final: 0.8500 (mptt) REVERT: A 549 ASP cc_start: 0.7974 (t70) cc_final: 0.7701 (t0) REVERT: B 328 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: B 407 GLN cc_start: 0.8942 (mt0) cc_final: 0.8674 (mm-40) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.4494 time to fit residues: 35.0561 Evaluate side-chains 70 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [68, 35, 60, 93, 53, 65, 44, 85, 89, 51, 32] chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 53 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.160651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121501 restraints weight = 9480.322| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.56 r_work: 0.3323 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8672 Z= 0.125 Angle : 0.541 7.039 12020 Z= 0.255 Chirality : 0.044 0.178 1375 Planarity : 0.004 0.039 1351 Dihedral : 10.571 70.595 1539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.97 % Allowed : 15.37 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.63 (0.28), residues: 929 helix: 2.00 (0.29), residues: 334 sheet: -0.86 (0.38), residues: 178 loop : -0.21 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.012 0.001 TYR A 183 PHE 0.011 0.001 PHE B 416 TRP 0.017 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8671) covalent geometry : angle 0.54136 / 0.25 (12020) hydrogen bonds : bond 0.03114 / 2.11 ( 390) hydrogen bonds : angle 4.79587 / 3.50 ( 1037) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.204 Fit side-chains REVERT: A 41 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5593 (mtt) REVERT: A 110 ASP cc_start: 0.7351 (p0) cc_final: 0.6978 (t0) REVERT: A 323 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7736 (mtmm) REVERT: A 356 ARG cc_start: 0.8333 (ttt-90) cc_final: 0.6829 (mpp-170) REVERT: A 388 LYS cc_start: 0.8115 (mttm) cc_final: 0.7476 (tptt) REVERT: A 431 LYS cc_start: 0.9029 (mttp) cc_final: 0.8500 (mptt) REVERT: A 549 ASP cc_start: 0.7984 (t70) cc_final: 0.7712 (t0) REVERT: B 328 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: B 407 GLN cc_start: 0.8926 (mt0) cc_final: 0.8604 (mm-40) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.4350 time to fit residues: 34.4196 Evaluate side-chains 70 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [59, 49, 27, 87, 42, 16, 76, 30, 60, 21, 89] chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.0270 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.160866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121704 restraints weight = 9387.113| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.55 r_work: 0.3324 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8672 Z= 0.123 Angle : 0.537 6.914 12020 Z= 0.253 Chirality : 0.044 0.176 1375 Planarity : 0.004 0.043 1351 Dihedral : 10.524 70.963 1539 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.58 % Allowed : 15.77 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.63 (0.28), residues: 929 helix: 1.99 (0.29), residues: 336 sheet: -0.87 (0.38), residues: 178 loop : -0.22 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.011 0.001 TYR A 183 PHE 0.011 0.001 PHE B 416 TRP 0.028 0.001 TRP A 406 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8671) covalent geometry : angle 0.53679 / 0.25 (12020) hydrogen bonds : bond 0.03089 / 2.09 ( 390) hydrogen bonds : angle 4.76077 / 3.47 ( 1037) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.306 Fit side-chains REVERT: A 41 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5535 (mtt) REVERT: A 110 ASP cc_start: 0.7338 (p0) cc_final: 0.6962 (t0) REVERT: A 323 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7723 (mtmm) REVERT: A 356 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.6700 (mpt180) REVERT: A 388 LYS cc_start: 0.8115 (mttm) cc_final: 0.7455 (tptt) REVERT: A 431 LYS cc_start: 0.9015 (mttp) cc_final: 0.8484 (mptt) REVERT: A 549 ASP cc_start: 0.7965 (t70) cc_final: 0.7671 (t0) REVERT: B 407 GLN cc_start: 0.8920 (mt0) cc_final: 0.8584 (mm-40) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.3904 time to fit residues: 29.5815 Evaluate side-chains 69 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [84, 17, 92, 54, 18, 93, 60, 77, 3, 29, 51] chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 92 optimal weight: 0.0170 chunk 54 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.160982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122036 restraints weight = 9387.461| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.54 r_work: 0.3330 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8672 Z= 0.120 Angle : 0.534 6.836 12020 Z= 0.252 Chirality : 0.044 0.175 1375 Planarity : 0.004 0.040 1351 Dihedral : 10.504 71.224 1539 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.10 % Allowed : 15.64 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.63 (0.28), residues: 929 helix: 1.98 (0.29), residues: 337 sheet: -0.87 (0.38), residues: 178 loop : -0.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.011 0.001 TYR A 183 PHE 0.011 0.001 PHE B 416 TRP 0.022 0.001 TRP A 406 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8671) covalent geometry : angle 0.53419 / 0.25 (12020) hydrogen bonds : bond 0.03070 / 2.07 ( 390) hydrogen bonds : angle 4.74542 / 3.46 ( 1037) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.278 Fit side-chains REVERT: A 41 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5639 (mtt) REVERT: A 110 ASP cc_start: 0.7315 (p0) cc_final: 0.6971 (t0) REVERT: A 323 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7758 (mtmm) REVERT: A 356 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.6793 (mpt180) REVERT: A 388 LYS cc_start: 0.8115 (mttm) cc_final: 0.7477 (tptt) REVERT: A 431 LYS cc_start: 0.9027 (mttp) cc_final: 0.8502 (mptt) REVERT: A 549 ASP cc_start: 0.7977 (t70) cc_final: 0.7699 (t0) REVERT: B 407 GLN cc_start: 0.8926 (mt0) cc_final: 0.8608 (mm-40) REVERT: B 413 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7931 (mm-30) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 0.3629 time to fit residues: 28.6752 Evaluate side-chains 71 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [73, 0, 77, 75, 28, 79, 6, 57, 31, 92, 87] chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123644 restraints weight = 9373.148| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.53 r_work: 0.3350 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8672 Z= 0.104 Angle : 0.529 10.356 12020 Z= 0.247 Chirality : 0.043 0.175 1375 Planarity : 0.004 0.039 1351 Dihedral : 10.440 71.748 1539 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.58 % Allowed : 16.16 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.67 (0.28), residues: 929 helix: 2.01 (0.29), residues: 339 sheet: -0.85 (0.38), residues: 178 loop : -0.20 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.010 0.001 TYR A 183 PHE 0.009 0.001 PHE B 416 TRP 0.021 0.001 TRP A 406 HIS 0.002 0.000 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 8671) covalent geometry : angle 0.52857 / 0.25 (12020) hydrogen bonds : bond 0.02951 / 1.99 ( 390) hydrogen bonds : angle 4.66014 / 3.40 ( 1037) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.285 Fit side-chains REVERT: A 110 ASP cc_start: 0.7273 (p0) cc_final: 0.6942 (t70) REVERT: A 323 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7769 (mtmm) REVERT: A 356 ARG cc_start: 0.8334 (ttt-90) cc_final: 0.6832 (mpt180) REVERT: A 388 LYS cc_start: 0.8105 (mttm) cc_final: 0.7491 (tptt) REVERT: A 431 LYS cc_start: 0.9010 (mttp) cc_final: 0.8506 (mptt) REVERT: A 549 ASP cc_start: 0.7937 (t70) cc_final: 0.7689 (t0) REVERT: B 40 GLU cc_start: 0.8118 (tp30) cc_final: 0.6980 (pt0) REVERT: B 407 GLN cc_start: 0.8921 (mt0) cc_final: 0.8617 (mm-40) REVERT: B 413 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7871 (mm-30) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.4289 time to fit residues: 31.8399 Evaluate side-chains 70 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [7, 47, 28, 12, 31, 90, 41, 77, 23, 69, 53] chunk 7 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 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 = 0.3822 r_free = 0.3822 target = 0.154178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112623 restraints weight = 9409.239| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.76 r_work: 0.3209 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8672 Z= 0.167 Angle : 0.568 10.056 12020 Z= 0.268 Chirality : 0.044 0.160 1375 Planarity : 0.004 0.041 1351 Dihedral : 10.594 71.038 1539 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.45 % Allowed : 16.16 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.28), residues: 929 helix: 1.87 (0.29), residues: 334 sheet: -0.89 (0.38), residues: 178 loop : -0.16 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.015 0.001 TYR A 183 PHE 0.013 0.001 PHE B 416 TRP 0.020 0.001 TRP A 406 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8671) covalent geometry : angle 0.56835 / 0.27 (12020) hydrogen bonds : bond 0.03304 / 2.24 ( 390) hydrogen bonds : angle 4.86640 / 3.55 ( 1037) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.98 seconds wall clock time: 45 minutes 14.82 seconds (2714.82 seconds total)