Starting phenix.real_space_refine on Thu Mar 13 02:42:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6k_36921/03_2025/8k6k_36921.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.017 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5416 2.51 5 N 1487 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8593 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4156 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1759 SG CYS A 226 52.458 65.121 35.741 1.00 68.72 S ATOM 1730 SG CYS A 222 53.553 69.898 31.737 1.00 73.94 S ATOM 1690 SG CYS A 216 51.999 64.698 29.070 1.00 67.33 S Time building chain proxies: 5.85, per 1000 atoms: 0.68 Number of scatterers: 8593 At special positions: 0 Unit cell: (104.06, 109.22, 76.54, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1487 7.00 C 5416 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 43.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.597A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.787A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.127A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.525A pdb=" N ASP A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.550A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.146A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.837A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 57 removed outlier: 4.225A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.536A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.861A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.654A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.643A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.901A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.747A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.339A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.164A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'C' and resid 387 through 388 338 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: 2.41 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8734 1.76 - 2.29: 90 2.29 - 2.83: 0 2.83 - 3.37: 0 3.37 - 3.91: 3 Bond restraints: 8827 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.45e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.814 -1.556 2.00e-02 2.50e+03 6.05e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.783 -1.550 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C8 U10 C 504 " pdb=" C9 U10 C 504 " ideal model delta sigma weight residual 1.470 1.323 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " ideal model delta sigma weight residual 1.334 1.479 -0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 8822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.48: 12051 9.48 - 18.96: 6 18.96 - 28.44: 0 28.44 - 37.92: 8 37.92 - 47.40: 2 Bond angle restraints: 12067 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.35 47.40 3.00e+00 1.11e-01 2.50e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 68.12 44.47 3.00e+00 1.11e-01 2.20e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 69.24 34.02 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.99 33.26 3.00e+00 1.11e-01 1.23e+02 angle pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 74.86 41.84 33.02 3.00e+00 1.11e-01 1.21e+02 ... (remaining 12062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4459 17.07 - 34.14: 531 34.14 - 51.21: 151 51.21 - 68.29: 59 68.29 - 85.36: 19 Dihedral angle restraints: 5219 sinusoidal: 2070 harmonic: 3149 Sorted by residual: dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -0.18 60.18 2 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" C2B HEC C 502 " pdb=" C3B HEC C 502 " pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sinusoidal sigma weight residual 60.00 0.04 59.96 2 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C2B HEC C 503 " pdb=" C3B HEC C 503 " pdb=" CAB HEC C 503 " pdb=" CBB HEC C 503 " ideal model delta sinusoidal sigma weight residual -120.00 -179.34 59.34 2 1.00e+01 1.00e-02 3.55e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.432: 1275 3.432 - 6.865: 0 6.865 - 10.297: 0 10.297 - 13.729: 0 13.729 - 17.162: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.39 17.16 2.00e-01 2.50e+01 7.36e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB THR C 328 " pdb=" CA THR C 328 " pdb=" OG1 THR C 328 " pdb=" CG2 THR C 328 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1273 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.016 2.00e-02 2.50e+03 8.61e-02 1.30e+02 pdb=" C1M U10 C 504 " -0.098 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.072 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.154 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.013 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO A 81 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 166 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 167 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.026 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8478 3.25 - 3.80: 15245 3.80 - 4.35: 20377 4.35 - 4.90: 32745 Nonbonded interactions: 77096 Sorted by model distance: nonbonded pdb=" O LEU C 154 " pdb=" OG SER C 159 " model vdw 2.147 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.208 3.040 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.254 2.688 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.255 2.688 ... (remaining 77091 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: 0.880 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.031 1.606 8827 Z= 1.373 Angle : 1.354 47.404 12067 Z= 0.502 Chirality : 0.483 17.162 1276 Planarity : 0.005 0.086 1566 Dihedral : 17.787 85.357 3209 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 18.33 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1082 helix: 1.69 (0.28), residues: 380 sheet: 0.66 (0.56), residues: 84 loop : -0.09 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.005 0.001 HIS B 64 PHE 0.016 0.001 PHE A 80 TYR 0.011 0.001 TYR A 443 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 MET cc_start: 0.8786 (tpt) cc_final: 0.7957 (tpt) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 1.3154 time to fit residues: 161.3758 Evaluate side-chains 112 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 306 ASN A 505 ASN A 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.060886 restraints weight = 12847.287| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.86 r_work: 0.2616 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 8827 Z= 0.373 Angle : 1.381 78.028 12067 Z= 0.507 Chirality : 0.097 3.068 1276 Planarity : 0.005 0.063 1566 Dihedral : 10.962 88.421 1306 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 16.86 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1082 helix: 1.82 (0.28), residues: 383 sheet: 0.27 (0.56), residues: 84 loop : -0.09 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS C 200 PHE 0.018 0.001 PHE A 270 TYR 0.011 0.001 TYR A 79 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8582 (tptm) REVERT: B 136 GLU cc_start: 0.8026 (pm20) cc_final: 0.7622 (pm20) REVERT: C 118 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8652 (tpt) outliers start: 23 outliers final: 9 residues processed: 122 average time/residue: 1.7668 time to fit residues: 229.3481 Evaluate side-chains 115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 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 303 ASN A 306 ASN A 505 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.063305 restraints weight = 13330.226| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.87 r_work: 0.2635 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 8827 Z= 0.251 Angle : 1.077 86.242 12067 Z= 0.410 Chirality : 0.058 1.329 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.509 89.372 1294 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.94 % Allowed : 15.84 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1082 helix: 1.87 (0.28), residues: 382 sheet: 0.12 (0.57), residues: 84 loop : -0.07 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8028 (pm20) cc_final: 0.7556 (pm20) REVERT: C 118 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8675 (tpt) outliers start: 26 outliers final: 11 residues processed: 125 average time/residue: 1.6851 time to fit residues: 224.4688 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 539 ASN B 123 GLN C 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.061104 restraints weight = 13328.768| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.02 r_work: 0.2577 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8827 Z= 0.278 Angle : 1.070 84.257 12067 Z= 0.408 Chirality : 0.060 1.425 1276 Planarity : 0.005 0.052 1566 Dihedral : 10.406 89.048 1294 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.15 % Allowed : 16.52 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1082 helix: 1.87 (0.28), residues: 384 sheet: 0.02 (0.57), residues: 84 loop : -0.08 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.016 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.004 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8028 (pm20) cc_final: 0.7475 (pm20) REVERT: C 118 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8741 (tpt) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 1.2481 time to fit residues: 154.2566 Evaluate side-chains 115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.075960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.059221 restraints weight = 13504.705| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.96 r_work: 0.2542 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 8827 Z= 0.349 Angle : 1.091 83.987 12067 Z= 0.420 Chirality : 0.062 1.440 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.538 88.462 1292 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.38 % Allowed : 16.63 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1082 helix: 1.81 (0.28), residues: 384 sheet: -0.04 (0.57), residues: 84 loop : -0.15 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 128 HIS 0.004 0.001 HIS C 200 PHE 0.024 0.001 PHE A 80 TYR 0.011 0.001 TYR A 79 ARG 0.007 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7982 (pm20) cc_final: 0.7413 (pm20) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 1.3230 time to fit residues: 166.3510 Evaluate side-chains 113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 1 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 303 ASN A 539 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.078650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.061701 restraints weight = 13469.943| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.00 r_work: 0.2589 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8827 Z= 0.249 Angle : 1.067 84.265 12067 Z= 0.404 Chirality : 0.060 1.407 1276 Planarity : 0.004 0.051 1566 Dihedral : 10.211 87.455 1292 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.81 % Allowed : 16.74 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1082 helix: 1.87 (0.28), residues: 390 sheet: -0.07 (0.58), residues: 84 loop : -0.14 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 278 PHE 0.015 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.004 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7968 (pm20) cc_final: 0.7364 (pm20) REVERT: C 118 MET cc_start: 0.9015 (tpt) cc_final: 0.8596 (tpt) outliers start: 16 outliers final: 11 residues processed: 119 average time/residue: 1.2230 time to fit residues: 155.2358 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 123 GLN C 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.078549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.061492 restraints weight = 13527.070| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.03 r_work: 0.2587 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8827 Z= 0.255 Angle : 1.069 83.901 12067 Z= 0.405 Chirality : 0.060 1.426 1276 Planarity : 0.005 0.050 1566 Dihedral : 10.206 87.823 1291 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.92 % Allowed : 17.19 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1082 helix: 1.88 (0.28), residues: 390 sheet: -0.04 (0.59), residues: 84 loop : -0.12 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE B 183 TYR 0.012 0.001 TYR A 443 ARG 0.004 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8001 (pm20) cc_final: 0.7445 (pm20) REVERT: C 118 MET cc_start: 0.9013 (tpt) cc_final: 0.8613 (tpt) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 1.2546 time to fit residues: 155.4911 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 91 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 539 ASN C 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.075920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.058826 restraints weight = 13780.686| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.00 r_work: 0.2533 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8827 Z= 0.379 Angle : 1.109 84.298 12067 Z= 0.426 Chirality : 0.062 1.416 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.516 88.537 1291 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.92 % Allowed : 17.19 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1082 helix: 1.76 (0.27), residues: 390 sheet: -0.06 (0.58), residues: 84 loop : -0.18 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 128 HIS 0.005 0.001 HIS C 89 PHE 0.027 0.001 PHE A 80 TYR 0.011 0.001 TYR A 79 ARG 0.002 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7986 (pm20) cc_final: 0.7454 (pm20) REVERT: B 140 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: C 118 MET cc_start: 0.9009 (tpt) cc_final: 0.8648 (tpt) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 1.2609 time to fit residues: 149.3502 Evaluate side-chains 113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.060978 restraints weight = 13556.552| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.03 r_work: 0.2573 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 8827 Z= 0.268 Angle : 1.081 84.343 12067 Z= 0.411 Chirality : 0.060 1.384 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.183 87.826 1291 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.81 % Allowed : 17.87 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1082 helix: 1.79 (0.27), residues: 392 sheet: -0.09 (0.59), residues: 84 loop : -0.19 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 PHE 0.016 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7989 (pm20) cc_final: 0.7422 (pm20) REVERT: C 118 MET cc_start: 0.8937 (tpt) cc_final: 0.8528 (tpt) REVERT: C 143 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8607 (mmtm) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 1.3079 time to fit residues: 161.5647 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 59 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.063814 restraints weight = 13370.313| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.03 r_work: 0.2630 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 8827 Z= 0.221 Angle : 1.067 84.507 12067 Z= 0.401 Chirality : 0.059 1.375 1276 Planarity : 0.004 0.050 1566 Dihedral : 9.816 87.240 1291 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.81 % Allowed : 17.87 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1082 helix: 1.85 (0.27), residues: 397 sheet: -0.03 (0.60), residues: 84 loop : -0.17 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8010 (pm20) cc_final: 0.7456 (pm20) REVERT: B 164 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6411 (m-70) REVERT: C 118 MET cc_start: 0.8927 (tpt) cc_final: 0.8533 (tpt) REVERT: C 143 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8636 (mmtp) REVERT: C 315 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6565 (p90) outliers start: 16 outliers final: 7 residues processed: 115 average time/residue: 1.2489 time to fit residues: 153.7211 Evaluate side-chains 114 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.063397 restraints weight = 13516.370| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.05 r_work: 0.2622 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 8827 Z= 0.227 Angle : 1.070 84.994 12067 Z= 0.403 Chirality : 0.058 1.340 1276 Planarity : 0.004 0.051 1566 Dihedral : 9.828 87.987 1291 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.36 % Allowed : 17.99 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1082 helix: 1.88 (0.27), residues: 397 sheet: 0.01 (0.59), residues: 84 loop : -0.15 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 PHE 0.014 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6716.17 seconds wall clock time: 117 minutes 5.74 seconds (7025.74 seconds total)