Starting phenix.real_space_refine on Wed Sep 17 06:30:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.map" model { file = "/net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4j_70103/09_2025/9o4j_70103.cif" } resolution = 3.06 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3804 2.51 5 N 1046 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5958 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3341 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2592 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.30 Number of scatterers: 5958 At special positions: 0 Unit cell: (60.1299, 85.5369, 101.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1083 8.00 N 1046 7.00 C 3804 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: 0.53 Conformation dependent library (CDL) restraints added in 337.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 3 sheets defined 48.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 76 removed outlier: 3.503A pdb=" N MET A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.252A pdb=" N LEU A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.763A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.956A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.640A pdb=" N ALA A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.603A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.747A pdb=" N GLU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 4.185A pdb=" N GLY A 428 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.624A pdb=" N LYS A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 486 through 506 removed outlier: 3.606A pdb=" N CYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 527 removed outlier: 3.605A pdb=" N SER A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 549 through 554 removed outlier: 4.115A pdb=" N SER A 552 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.550A pdb=" N VAL B 15 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.583A pdb=" N GLY B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 4.602A pdb=" N HIS B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.812A pdb=" N LEU B 76 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 77 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 190 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 213 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 286 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER B 281 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N MET B 312 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 283 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 285 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.739A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 393 removed outlier: 6.739A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP A 569 " --> pdb=" O PRO A 573 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1053 1.32 - 1.44: 1568 1.44 - 1.56: 3440 1.56 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6100 Sorted by residual: bond pdb=" CB ASN A 102 " pdb=" CG ASN A 102 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 bond pdb=" CB GLU A 422 " pdb=" CG GLU A 422 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.44e-01 bond pdb=" CA THR A 571 " pdb=" C THR A 571 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.35e-02 5.49e+03 8.51e-01 bond pdb=" CD GLU B 98 " pdb=" OE1 GLU B 98 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.30e-01 bond pdb=" C SER A 277 " pdb=" N PRO A 278 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.18e-02 7.18e+03 8.29e-01 ... (remaining 6095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 8177 2.34 - 4.68: 124 4.68 - 7.02: 14 7.02 - 9.35: 0 9.35 - 11.69: 1 Bond angle restraints: 8316 Sorted by residual: angle pdb=" CA LEU A 345 " pdb=" CB LEU A 345 " pdb=" CG LEU A 345 " ideal model delta sigma weight residual 116.30 127.99 -11.69 3.50e+00 8.16e-02 1.12e+01 angle pdb=" C SER B 191 " pdb=" CA SER B 191 " pdb=" CB SER B 191 " ideal model delta sigma weight residual 110.42 116.39 -5.97 1.99e+00 2.53e-01 9.01e+00 angle pdb=" CA GLU B 98 " pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.63e+00 angle pdb=" CA GLU A 106 " pdb=" CB GLU A 106 " pdb=" CG GLU A 106 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" CA THR A 571 " pdb=" CB THR A 571 " pdb=" CG2 THR A 571 " ideal model delta sigma weight residual 110.50 115.26 -4.76 1.70e+00 3.46e-01 7.83e+00 ... (remaining 8311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3230 17.95 - 35.90: 347 35.90 - 53.85: 84 53.85 - 71.80: 17 71.80 - 89.75: 5 Dihedral angle restraints: 3683 sinusoidal: 1423 harmonic: 2260 Sorted by residual: dihedral pdb=" CA THR A 298 " pdb=" C THR A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP B 128 " pdb=" CB ASP B 128 " pdb=" CG ASP B 128 " pdb=" OD1 ASP B 128 " ideal model delta sinusoidal sigma weight residual -30.00 -88.82 58.82 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " pdb=" CD GLU A 513 " pdb=" OE1 GLU A 513 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 570 0.033 - 0.065: 237 0.065 - 0.098: 80 0.098 - 0.131: 41 0.131 - 0.163: 11 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB ILE B 94 " pdb=" CA ILE B 94 " pdb=" CG1 ILE B 94 " pdb=" CG2 ILE B 94 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CG LEU A 345 " pdb=" CB LEU A 345 " pdb=" CD1 LEU A 345 " pdb=" CD2 LEU A 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 936 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 126 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ILE B 126 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 126 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR B 127 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 571 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C THR A 571 " 0.036 2.00e-02 2.50e+03 pdb=" O THR A 571 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 572 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 80 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C GLY A 80 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 80 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 81 " 0.011 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3104 3.00 - 3.48: 5698 3.48 - 3.95: 9026 3.95 - 4.43: 10368 4.43 - 4.90: 17294 Nonbonded interactions: 45490 Sorted by model distance: nonbonded pdb=" N ASP A 399 " pdb=" OD1 ASP A 399 " model vdw 2.526 3.120 nonbonded pdb=" O ASP A 44 " pdb=" OD1 ASP A 44 " model vdw 2.537 3.040 nonbonded pdb=" O ASP B 61 " pdb=" OD1 ASP B 61 " model vdw 2.576 3.040 nonbonded pdb=" OE1 GLN A 292 " pdb=" OD1 ASN A 331 " model vdw 2.581 3.040 nonbonded pdb=" CG LYS A 65 " pdb=" NZ LYS A 65 " model vdw 2.588 2.816 ... (remaining 45485 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6100 Z= 0.173 Angle : 0.678 11.692 8316 Z= 0.367 Chirality : 0.046 0.163 939 Planarity : 0.004 0.040 1078 Dihedral : 15.968 89.754 2225 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.00 % Allowed : 21.63 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.30), residues: 775 helix: 1.21 (0.28), residues: 354 sheet: 0.69 (0.52), residues: 104 loop : -1.90 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.015 0.002 TYR A 473 PHE 0.019 0.002 PHE B 238 TRP 0.029 0.002 TRP B 246 HIS 0.005 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6100) covalent geometry : angle 0.67809 ( 8316) hydrogen bonds : bond 0.16472 ( 305) hydrogen bonds : angle 6.36080 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 491 MET cc_start: 0.9400 (mmt) cc_final: 0.9185 (mmm) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.0868 time to fit residues: 11.0238 Evaluate side-chains 62 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 149 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072714 restraints weight = 12648.259| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.44 r_work: 0.2836 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6100 Z= 0.128 Angle : 0.539 6.096 8316 Z= 0.288 Chirality : 0.041 0.154 939 Planarity : 0.004 0.041 1078 Dihedral : 4.579 52.287 938 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.50 % Allowed : 19.63 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.31), residues: 775 helix: 1.88 (0.28), residues: 348 sheet: 0.93 (0.53), residues: 104 loop : -1.43 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.015 0.001 TYR A 296 PHE 0.015 0.002 PHE B 238 TRP 0.014 0.001 TRP B 246 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6100) covalent geometry : angle 0.53895 ( 8316) hydrogen bonds : bond 0.04486 ( 305) hydrogen bonds : angle 4.70377 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 HIS cc_start: 0.8030 (m-70) cc_final: 0.7824 (m-70) REVERT: A 491 MET cc_start: 0.9165 (mmt) cc_final: 0.8919 (mmm) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.0614 time to fit residues: 6.0331 Evaluate side-chains 59 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072105 restraints weight = 12678.582| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.55 r_work: 0.2905 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6100 Z= 0.124 Angle : 0.482 5.252 8316 Z= 0.258 Chirality : 0.040 0.145 939 Planarity : 0.004 0.052 1078 Dihedral : 4.033 47.425 928 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.16 % Allowed : 16.81 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.32), residues: 775 helix: 2.08 (0.28), residues: 349 sheet: 1.00 (0.54), residues: 106 loop : -1.19 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 82 TYR 0.012 0.001 TYR A 296 PHE 0.014 0.001 PHE B 238 TRP 0.008 0.001 TRP A 569 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6100) covalent geometry : angle 0.48221 ( 8316) hydrogen bonds : bond 0.03994 ( 305) hydrogen bonds : angle 4.27199 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.250 Fit side-chains REVERT: A 294 HIS cc_start: 0.8120 (m-70) cc_final: 0.7767 (m-70) REVERT: A 491 MET cc_start: 0.9181 (mmt) cc_final: 0.8931 (mmm) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.0605 time to fit residues: 5.6903 Evaluate side-chains 63 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 50 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074528 restraints weight = 12616.829| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.54 r_work: 0.2873 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6100 Z= 0.087 Angle : 0.466 11.393 8316 Z= 0.239 Chirality : 0.039 0.139 939 Planarity : 0.004 0.057 1078 Dihedral : 3.495 17.044 925 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 18.30 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.32), residues: 775 helix: 2.29 (0.28), residues: 350 sheet: 1.02 (0.53), residues: 107 loop : -1.03 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 73 TYR 0.011 0.001 TYR A 296 PHE 0.011 0.001 PHE B 64 TRP 0.005 0.001 TRP A 99 HIS 0.002 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 6100) covalent geometry : angle 0.46554 ( 8316) hydrogen bonds : bond 0.03076 ( 305) hydrogen bonds : angle 3.92259 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 294 HIS cc_start: 0.8172 (m-70) cc_final: 0.7739 (m-70) REVERT: A 491 MET cc_start: 0.9093 (mmt) cc_final: 0.8888 (mmm) REVERT: B 73 ARG cc_start: 0.8466 (mtm110) cc_final: 0.7959 (mtm-85) outliers start: 14 outliers final: 9 residues processed: 63 average time/residue: 0.0673 time to fit residues: 6.2435 Evaluate side-chains 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070805 restraints weight = 13014.343| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.48 r_work: 0.2780 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6100 Z= 0.173 Angle : 0.521 9.530 8316 Z= 0.270 Chirality : 0.041 0.133 939 Planarity : 0.004 0.062 1078 Dihedral : 3.704 17.112 924 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.50 % Allowed : 18.30 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.32), residues: 775 helix: 2.17 (0.28), residues: 353 sheet: 0.95 (0.53), residues: 107 loop : -0.91 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 73 TYR 0.013 0.001 TYR B 155 PHE 0.019 0.002 PHE B 238 TRP 0.008 0.001 TRP A 569 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6100) covalent geometry : angle 0.52119 ( 8316) hydrogen bonds : bond 0.04418 ( 305) hydrogen bonds : angle 4.16441 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.266 Fit side-chains REVERT: A 294 HIS cc_start: 0.8251 (m-70) cc_final: 0.8022 (m90) REVERT: A 491 MET cc_start: 0.9141 (mmt) cc_final: 0.8887 (mmm) REVERT: B 73 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8161 (mtm110) outliers start: 15 outliers final: 14 residues processed: 62 average time/residue: 0.0676 time to fit residues: 6.0639 Evaluate side-chains 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072415 restraints weight = 12731.462| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.55 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6100 Z= 0.091 Angle : 0.459 7.612 8316 Z= 0.237 Chirality : 0.039 0.134 939 Planarity : 0.004 0.054 1078 Dihedral : 3.465 16.061 924 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 18.47 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.32), residues: 775 helix: 2.34 (0.28), residues: 352 sheet: 0.99 (0.53), residues: 107 loop : -0.83 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.011 0.001 TYR B 155 PHE 0.012 0.001 PHE A 295 TRP 0.006 0.001 TRP A 569 HIS 0.003 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 6100) covalent geometry : angle 0.45890 ( 8316) hydrogen bonds : bond 0.03191 ( 305) hydrogen bonds : angle 3.87347 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 223 HIS cc_start: 0.8972 (m90) cc_final: 0.8504 (m90) REVERT: A 294 HIS cc_start: 0.8358 (m-70) cc_final: 0.8055 (m90) REVERT: A 299 CYS cc_start: 0.6711 (p) cc_final: 0.6360 (p) REVERT: A 374 CYS cc_start: 0.8991 (t) cc_final: 0.8636 (p) REVERT: A 401 ASP cc_start: 0.8935 (t0) cc_final: 0.8529 (t70) REVERT: A 491 MET cc_start: 0.9137 (mmt) cc_final: 0.8927 (mmm) REVERT: B 73 ARG cc_start: 0.8522 (mtm110) cc_final: 0.8167 (mtm110) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.0675 time to fit residues: 6.4251 Evaluate side-chains 63 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071784 restraints weight = 12818.486| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.55 r_work: 0.2888 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6100 Z= 0.104 Angle : 0.465 6.923 8316 Z= 0.240 Chirality : 0.039 0.132 939 Planarity : 0.004 0.057 1078 Dihedral : 3.421 16.960 924 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.50 % Allowed : 19.30 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.32), residues: 775 helix: 2.45 (0.28), residues: 350 sheet: 1.00 (0.53), residues: 107 loop : -0.79 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.013 0.001 TYR B 155 PHE 0.012 0.001 PHE B 238 TRP 0.006 0.001 TRP A 569 HIS 0.002 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6100) covalent geometry : angle 0.46519 ( 8316) hydrogen bonds : bond 0.03386 ( 305) hydrogen bonds : angle 3.84735 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.155 Fit side-chains REVERT: A 59 MET cc_start: 0.8609 (mmt) cc_final: 0.8372 (mmt) REVERT: A 294 HIS cc_start: 0.8416 (m-70) cc_final: 0.8062 (m90) REVERT: A 299 CYS cc_start: 0.6642 (p) cc_final: 0.6385 (p) REVERT: A 374 CYS cc_start: 0.8999 (t) cc_final: 0.8635 (p) REVERT: A 401 ASP cc_start: 0.8956 (t0) cc_final: 0.8535 (t70) REVERT: A 491 MET cc_start: 0.9133 (mmt) cc_final: 0.8841 (mmm) REVERT: B 73 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8207 (mtm110) outliers start: 15 outliers final: 14 residues processed: 61 average time/residue: 0.0578 time to fit residues: 5.3463 Evaluate side-chains 62 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071439 restraints weight = 12727.249| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.54 r_work: 0.2882 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6100 Z= 0.109 Angle : 0.468 6.342 8316 Z= 0.243 Chirality : 0.039 0.134 939 Planarity : 0.004 0.054 1078 Dihedral : 3.428 15.957 924 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.50 % Allowed : 19.80 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.31), residues: 775 helix: 2.48 (0.28), residues: 349 sheet: 0.98 (0.53), residues: 107 loop : -0.77 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.012 0.001 TYR B 155 PHE 0.014 0.001 PHE A 295 TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6100) covalent geometry : angle 0.46814 ( 8316) hydrogen bonds : bond 0.03436 ( 305) hydrogen bonds : angle 3.84521 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.242 Fit side-chains REVERT: A 59 MET cc_start: 0.8654 (mmt) cc_final: 0.8376 (mmt) REVERT: A 294 HIS cc_start: 0.8461 (m-70) cc_final: 0.7810 (m-70) REVERT: A 299 CYS cc_start: 0.6797 (p) cc_final: 0.6534 (p) REVERT: A 491 MET cc_start: 0.9149 (mmt) cc_final: 0.8861 (mmm) REVERT: B 73 ARG cc_start: 0.8531 (mtm110) cc_final: 0.8248 (mtm110) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.0631 time to fit residues: 5.4067 Evaluate side-chains 59 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.0010 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072419 restraints weight = 12783.117| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.56 r_work: 0.2899 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6100 Z= 0.094 Angle : 0.453 6.746 8316 Z= 0.235 Chirality : 0.039 0.128 939 Planarity : 0.004 0.054 1078 Dihedral : 3.317 16.430 924 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.16 % Allowed : 20.13 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.32), residues: 775 helix: 2.55 (0.28), residues: 350 sheet: 0.98 (0.53), residues: 107 loop : -0.67 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.014 0.001 TYR B 155 PHE 0.013 0.001 PHE A 295 TRP 0.006 0.001 TRP A 569 HIS 0.002 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6100) covalent geometry : angle 0.45303 ( 8316) hydrogen bonds : bond 0.03085 ( 305) hydrogen bonds : angle 3.74221 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.251 Fit side-chains REVERT: A 59 MET cc_start: 0.8705 (mmt) cc_final: 0.8433 (mmt) REVERT: A 294 HIS cc_start: 0.8522 (m-70) cc_final: 0.7847 (m-70) REVERT: A 299 CYS cc_start: 0.6849 (p) cc_final: 0.6560 (p) REVERT: A 374 CYS cc_start: 0.8984 (t) cc_final: 0.8703 (p) REVERT: B 73 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8244 (mtm110) outliers start: 13 outliers final: 13 residues processed: 63 average time/residue: 0.0663 time to fit residues: 6.1216 Evaluate side-chains 65 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072498 restraints weight = 12916.397| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.58 r_work: 0.2900 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6100 Z= 0.095 Angle : 0.469 6.869 8316 Z= 0.243 Chirality : 0.039 0.128 939 Planarity : 0.004 0.054 1078 Dihedral : 3.300 15.785 924 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.33 % Allowed : 19.97 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.31), residues: 775 helix: 2.52 (0.28), residues: 350 sheet: 0.99 (0.53), residues: 107 loop : -0.65 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.013 0.001 TYR B 155 PHE 0.013 0.001 PHE A 295 TRP 0.007 0.001 TRP A 569 HIS 0.002 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6100) covalent geometry : angle 0.46936 ( 8316) hydrogen bonds : bond 0.03150 ( 305) hydrogen bonds : angle 3.78396 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8688 (mmt) cc_final: 0.8410 (mmt) REVERT: A 294 HIS cc_start: 0.8525 (m-70) cc_final: 0.7852 (m-70) REVERT: A 299 CYS cc_start: 0.6845 (p) cc_final: 0.6538 (p) REVERT: A 374 CYS cc_start: 0.8985 (t) cc_final: 0.8704 (p) REVERT: A 491 MET cc_start: 0.9088 (mmm) cc_final: 0.8787 (mmm) REVERT: B 73 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8283 (mtm110) outliers start: 14 outliers final: 13 residues processed: 60 average time/residue: 0.0681 time to fit residues: 5.9499 Evaluate side-chains 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071787 restraints weight = 12708.501| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.54 r_work: 0.2888 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6100 Z= 0.104 Angle : 0.501 15.694 8316 Z= 0.251 Chirality : 0.039 0.128 939 Planarity : 0.004 0.054 1078 Dihedral : 3.321 15.812 924 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.00 % Allowed : 20.13 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.31), residues: 775 helix: 2.52 (0.28), residues: 350 sheet: 1.01 (0.53), residues: 107 loop : -0.64 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 207 TYR 0.013 0.001 TYR B 155 PHE 0.013 0.001 PHE A 295 TRP 0.006 0.001 TRP A 569 HIS 0.002 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6100) covalent geometry : angle 0.50110 ( 8316) hydrogen bonds : bond 0.03315 ( 305) hydrogen bonds : angle 3.81922 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.14 seconds wall clock time: 27 minutes 7.86 seconds (1627.86 seconds total)