Starting phenix.real_space_refine on Tue Apr 29 09:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6k_36921/04_2025/8k6k_36921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6k_36921/04_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_36921/04_2025/8k6k_36921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6k_36921/04_2025/8k6k_36921.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6k_36921/04_2025/8k6k_36921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6k_36921/04_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-5669/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: 5.94, per 1000 atoms: 0.69 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: 2.91 Conformation dependent library (CDL) restraints added in 931.5 milliseconds 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: 0.92 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: 2.43 Time building geometry restraints manager: 3.08 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: 1.540 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 25.730 Find NCS groups from input model: 0.070 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- 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 8842 Z= 1.640 Angle : 1.364 47.404 12076 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 Details of bonding type rmsd hydrogen bonds : bond 0.15747 ( 331) hydrogen bonds : angle 6.92057 ( 921) metal coordination : bond 0.00163 ( 3) metal coordination : angle 6.25523 ( 9) covalent geometry : bond 0.03050 ( 8827) covalent geometry : angle 1.35409 (12067) Misc. bond : bond 0.17079 ( 12) *********************** 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 : 1.306 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: 1.2639 time to fit residues: 155.2994 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 : 0.941 ------------------------------------------------------------------------------- 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 8842 Z= 0.251 Angle : 1.574 78.028 12076 Z= 0.511 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 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 331) hydrogen bonds : angle 5.54322 ( 921) metal coordination : bond 0.01309 ( 3) metal coordination : angle 27.68838 ( 9) covalent geometry : bond 0.00568 ( 8827) covalent geometry : angle 1.38125 (12067) Misc. bond : bond 0.05959 ( 12) *********************** 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 : 0.944 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: 1.3252 time to fit residues: 171.9254 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 : 1.008 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.2991 r_free = 0.2991 target = 0.078588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.062525 restraints weight = 13516.167| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.90 r_work: 0.2634 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 8842 Z= 0.156 Angle : 1.466 87.254 12076 Z= 0.419 Chirality : 0.058 1.346 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.499 89.334 1294 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: 0.93 (0.26), residues: 1082 helix: 1.88 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 331) hydrogen bonds : angle 5.28289 ( 921) metal coordination : bond 0.00812 ( 3) metal coordination : angle 36.28474 ( 9) covalent geometry : bond 0.00372 ( 8827) covalent geometry : angle 1.08093 (12067) Misc. bond : bond 0.05103 ( 12) *********************** 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 : 0.961 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8026 (pm20) cc_final: 0.7553 (pm20) REVERT: C 118 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8676 (tpt) outliers start: 26 outliers final: 11 residues processed: 125 average time/residue: 1.7846 time to fit residues: 236.7120 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 : 0.863 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.2940 r_free = 0.2940 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.060041 restraints weight = 13405.456| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 1.96 r_work: 0.2558 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 8842 Z= 0.196 Angle : 1.451 84.371 12076 Z= 0.422 Chirality : 0.061 1.419 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.501 88.684 1294 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 16.63 % 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: 0.86 (0.26), residues: 1082 helix: 1.83 (0.28), residues: 384 sheet: -0.02 (0.57), residues: 84 loop : -0.10 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 PHE 0.019 0.001 PHE A 80 TYR 0.011 0.001 TYR A 443 ARG 0.003 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 331) hydrogen bonds : angle 5.22582 ( 921) metal coordination : bond 0.00423 ( 3) metal coordination : angle 35.44397 ( 9) covalent geometry : bond 0.00469 ( 8827) covalent geometry : angle 1.08213 (12067) Misc. bond : bond 0.06405 ( 12) *********************** 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 126 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8022 (pm20) cc_final: 0.7470 (pm20) REVERT: C 118 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8766 (tpt) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 1.3631 time to fit residues: 169.9026 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 : 0.947 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 81 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.0000 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.2934 r_free = 0.2934 target = 0.076420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.059696 restraints weight = 13462.124| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 1.97 r_work: 0.2552 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.183 8842 Z= 0.203 Angle : 1.466 84.096 12076 Z= 0.424 Chirality : 0.062 1.437 1276 Planarity : 0.005 0.055 1566 Dihedral : 10.443 88.095 1292 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 16.63 % 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: 0.80 (0.26), residues: 1082 helix: 1.80 (0.28), residues: 384 sheet: -0.09 (0.57), residues: 84 loop : -0.15 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 PHE 0.020 0.001 PHE A 80 TYR 0.012 0.001 TYR A 79 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 331) hydrogen bonds : angle 5.19932 ( 921) metal coordination : bond 0.00442 ( 3) metal coordination : angle 36.06914 ( 9) covalent geometry : bond 0.00486 ( 8827) covalent geometry : angle 1.08583 (12067) Misc. bond : bond 0.07112 ( 12) *********************** 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 129 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7997 (pm20) cc_final: 0.7467 (pm20) REVERT: C 118 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8780 (tpt) outliers start: 22 outliers final: 10 residues processed: 121 average time/residue: 1.2813 time to fit residues: 165.1139 Evaluate side-chains 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 118 MET 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: 1.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.2954 r_free = 0.2954 target = 0.077374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.060596 restraints weight = 13458.310| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.99 r_work: 0.2564 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 8842 Z= 0.179 Angle : 1.373 84.357 12076 Z= 0.416 Chirality : 0.060 1.409 1276 Planarity : 0.005 0.054 1566 Dihedral : 10.336 87.841 1292 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.81 % Allowed : 17.08 % Favored : 81.11 % 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: 0.81 (0.26), residues: 1082 helix: 1.82 (0.28), residues: 390 sheet: -0.11 (0.58), residues: 84 loop : -0.18 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 331) hydrogen bonds : angle 5.13079 ( 921) metal coordination : bond 0.00375 ( 3) metal coordination : angle 31.09531 ( 9) covalent geometry : bond 0.00424 ( 8827) covalent geometry : angle 1.07900 (12067) Misc. bond : bond 0.06626 ( 12) *********************** 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 123 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7964 (pm20) cc_final: 0.7366 (pm20) REVERT: C 118 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8784 (tpt) outliers start: 16 outliers final: 11 residues processed: 117 average time/residue: 1.3726 time to fit residues: 171.1046 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 : 0.983 ------------------------------------------------------------------------------- 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 118 MET 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: 0.9980 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.078701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.061621 restraints weight = 13526.257| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.02 r_work: 0.2589 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 8842 Z= 0.159 Angle : 1.344 84.035 12076 Z= 0.410 Chirality : 0.060 1.418 1276 Planarity : 0.005 0.052 1566 Dihedral : 10.200 87.301 1291 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 16.74 % 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: 0.81 (0.26), residues: 1082 helix: 1.85 (0.28), residues: 392 sheet: -0.09 (0.58), residues: 84 loop : -0.20 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS C 89 PHE 0.016 0.001 PHE B 183 TYR 0.013 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 331) hydrogen bonds : angle 5.03525 ( 921) metal coordination : bond 0.00361 ( 3) metal coordination : angle 29.87888 ( 9) covalent geometry : bond 0.00373 ( 8827) covalent geometry : angle 1.06850 (12067) Misc. bond : bond 0.05659 ( 12) *********************** 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 128 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7994 (pm20) cc_final: 0.7444 (pm20) REVERT: B 140 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (mttm) REVERT: C 118 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (tpt) outliers start: 20 outliers final: 11 residues processed: 119 average time/residue: 1.2288 time to fit residues: 156.1487 Evaluate side-chains 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET 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: 0.9990 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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 B 123 GLN C 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.061228 restraints weight = 13682.205| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.04 r_work: 0.2579 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 8842 Z= 0.169 Angle : 1.344 84.055 12076 Z= 0.413 Chirality : 0.060 1.419 1276 Planarity : 0.005 0.050 1566 Dihedral : 10.185 87.624 1291 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.15 % Allowed : 17.19 % 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: 0.87 (0.26), residues: 1082 helix: 1.87 (0.27), residues: 390 sheet: -0.08 (0.58), residues: 84 loop : -0.14 (0.26), residues: 608 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 0.015 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 331) hydrogen bonds : angle 5.04182 ( 921) metal coordination : bond 0.00365 ( 3) metal coordination : angle 29.59022 ( 9) covalent geometry : bond 0.00397 ( 8827) covalent geometry : angle 1.07512 (12067) Misc. bond : bond 0.06111 ( 12) *********************** 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 126 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8021 (pm20) cc_final: 0.7488 (pm20) REVERT: B 140 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (mttm) REVERT: C 118 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8787 (tpt) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 1.2705 time to fit residues: 157.2026 Evaluate side-chains 119 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 140 LYS 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 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.075514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.058280 restraints weight = 13691.239| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 2.01 r_work: 0.2520 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.206 8842 Z= 0.261 Angle : 1.388 84.197 12076 Z= 0.438 Chirality : 0.063 1.412 1276 Planarity : 0.005 0.052 1566 Dihedral : 10.569 88.854 1291 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.81 % Allowed : 17.76 % Favored : 80.43 % 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: 0.74 (0.26), residues: 1082 helix: 1.76 (0.27), residues: 384 sheet: -0.09 (0.58), residues: 84 loop : -0.20 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 128 HIS 0.005 0.001 HIS C 89 PHE 0.031 0.002 PHE A 80 TYR 0.012 0.002 TYR A 79 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 331) hydrogen bonds : angle 5.25016 ( 921) metal coordination : bond 0.00474 ( 3) metal coordination : angle 30.06978 ( 9) covalent geometry : bond 0.00625 ( 8827) covalent geometry : angle 1.12014 (12067) Misc. bond : bond 0.08746 ( 12) *********************** 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 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 539 ASN cc_start: 0.8963 (t0) cc_final: 0.8750 (t0) REVERT: B 136 GLU cc_start: 0.7971 (pm20) cc_final: 0.7439 (pm20) REVERT: B 140 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (mttm) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 1.4504 time to fit residues: 166.8882 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 : 0.905 ------------------------------------------------------------------------------- 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 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 140 LYS 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: 4.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.078695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.061627 restraints weight = 13475.909| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.03 r_work: 0.2588 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 8842 Z= 0.156 Angle : 1.345 84.694 12076 Z= 0.414 Chirality : 0.059 1.365 1276 Planarity : 0.005 0.052 1566 Dihedral : 10.095 87.574 1291 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.70 % Allowed : 17.87 % Favored : 80.43 % 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: 1.82 (0.27), residues: 392 sheet: -0.12 (0.58), residues: 84 loop : -0.21 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 331) hydrogen bonds : angle 5.06584 ( 921) metal coordination : bond 0.00415 ( 3) metal coordination : angle 29.04494 ( 9) covalent geometry : bond 0.00362 ( 8827) covalent geometry : angle 1.08648 (12067) Misc. bond : bond 0.07580 ( 12) ********************** 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 120 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.8030 (pm20) cc_final: 0.7480 (pm20) REVERT: B 140 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8495 (mttm) REVERT: C 118 MET cc_start: 0.8963 (tpt) cc_final: 0.8501 (tpt) REVERT: C 143 LYS cc_start: 0.8982 (ptmm) cc_final: 0.8607 (mmtm) REVERT: C 315 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6496 (p90) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 1.2187 time to fit residues: 148.4208 Evaluate side-chains 114 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 112 MET Chi-restraints excluded: chain B residue 140 LYS 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 30 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 68 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.063005 restraints weight = 13573.699| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.05 r_work: 0.2615 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 8842 Z= 0.145 Angle : 1.288 85.782 12076 Z= 0.410 Chirality : 0.058 1.314 1276 Planarity : 0.004 0.049 1566 Dihedral : 9.886 87.511 1291 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.70 % Allowed : 17.65 % 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: 0.86 (0.26), residues: 1082 helix: 1.87 (0.27), residues: 396 sheet: -0.05 (0.59), residues: 84 loop : -0.19 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.014 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 331) hydrogen bonds : angle 4.90988 ( 921) metal coordination : bond 0.00520 ( 3) metal coordination : angle 25.53361 ( 9) covalent geometry : bond 0.00334 ( 8827) covalent geometry : angle 1.08348 (12067) Misc. bond : bond 0.05576 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.00 seconds wall clock time: 124 minutes 3.45 seconds (7443.45 seconds total)