Starting phenix.real_space_refine on Wed Mar 4 03:14:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k32_62004/03_2026/9k32_62004.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 208 5.49 5 Mg 3 5.21 5 S 24 5.16 5 C 5698 2.51 5 N 1892 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10323 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 733, 5916 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 710} Conformer: "B" Number of residues, atoms: 733, 5916 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 710} bond proxies already assigned to first conformer: 5997 Chain: "B" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3262 Classifications: {'RNA': 153} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 74, 'rna3p_pyr': 64} Link IDs: {'rna2p': 15, 'rna3p': 137} Chain breaks: 2 Chain: "C" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 702 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 421 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 9} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1418 SG CYS A 172 43.508 52.091 109.117 1.00 22.62 S ATOM 1440 SG CYS A 175 39.932 51.882 109.811 1.00 25.02 S ATOM 2084 SG CYS A 253 41.638 55.130 110.527 1.00 26.91 S ATOM 2854 SG CYS A 348 66.322 71.565 69.486 1.00 42.36 S ATOM 2879 SG CYS A 351 66.146 73.344 65.888 1.00 47.30 S ATOM 3106 SG CYS A 383 62.923 72.228 67.550 1.00 42.62 S ATOM 3129 SG CYS A 386 65.374 70.421 65.758 1.00 44.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASN A 632 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 632 " occ=0.50 Time building chain proxies: 3.40, per 1000 atoms: 0.33 Number of scatterers: 10323 At special positions: 0 Unit cell: (99.6, 102.92, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 24 16.00 P 208 15.00 Mg 3 11.99 O 2496 8.00 N 1892 7.00 C 5698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 577.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 256 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 172 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 253 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 175 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 383 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 386 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 348 " Number of angles added : 9 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 45.4% alpha, 15.8% beta 87 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 39 through 74 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.704A pdb=" N GLU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 181 through 184 Processing helix chain 'A' and resid 185 through 195 removed outlier: 3.900A pdb=" N ILE A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.575A pdb=" N GLU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.865A pdb=" N ASN A 237 " --> pdb=" O TRP A 233 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.604A pdb=" N ALA A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.580A pdb=" N VAL A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.543A pdb=" N TYR A 325 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.511A pdb=" N THR A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.891A pdb=" N SER A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.528A pdb=" N LEU A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.763A pdb=" N ALA A 571 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.746A pdb=" N VAL A 604 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing sheet with id=AA1, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.116A pdb=" N LEU A 5 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 302 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 7 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU A 304 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE A 9 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP A 22 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 28 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.116A pdb=" N LEU A 5 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 302 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 7 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU A 304 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE A 9 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP A 22 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 28 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 364 Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 630 Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.912A pdb=" N GLY A 643 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU A 648 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 679 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 698 Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 715 removed outlier: 3.757A pdb=" N ASP A 709 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 217 hydrogen bonds 394 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 138 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1845 1.34 - 1.46: 3843 1.46 - 1.58: 4773 1.58 - 1.70: 420 1.70 - 1.82: 37 Bond restraints: 10918 Sorted by residual: bond pdb=" C LEU A 197 " pdb=" N PRO A 198 " ideal model delta sigma weight residual 1.334 1.371 -0.037 8.40e-03 1.42e+04 1.96e+01 bond pdb=" C LYS A 510 " pdb=" N PRO A 511 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.27e-02 6.20e+03 1.25e+01 bond pdb=" C MET A 100 " pdb=" N PRO A 101 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C MET A 293 " pdb=" N PRO A 294 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.28e-02 6.10e+03 1.08e+01 bond pdb=" C GLU A 670 " pdb=" N PRO A 671 " ideal model delta sigma weight residual 1.328 1.368 -0.040 1.26e-02 6.30e+03 9.87e+00 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13095 1.98 - 3.96: 2291 3.96 - 5.94: 243 5.94 - 7.92: 24 7.92 - 9.90: 1 Bond angle restraints: 15654 Sorted by residual: angle pdb=" CA PHE A 228 " pdb=" CB PHE A 228 " pdb=" CG PHE A 228 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" O3' A B 117 " pdb=" C3' A B 117 " pdb=" C2' A B 117 " ideal model delta sigma weight residual 109.50 116.98 -7.48 1.50e+00 4.44e-01 2.49e+01 angle pdb=" C GLU A 331 " pdb=" CA GLU A 331 " pdb=" CB GLU A 331 " ideal model delta sigma weight residual 109.68 119.58 -9.90 2.05e+00 2.38e-01 2.33e+01 angle pdb=" CA ASP A 544 " pdb=" CB ASP A 544 " pdb=" CG ASP A 544 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" N LYS A 61 " pdb=" CA LYS A 61 " pdb=" CB LYS A 61 " ideal model delta sigma weight residual 110.12 116.95 -6.83 1.47e+00 4.63e-01 2.16e+01 ... (remaining 15649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5570 17.22 - 34.44: 640 34.44 - 51.66: 221 51.66 - 68.88: 207 68.88 - 86.10: 38 Dihedral angle restraints: 6676 sinusoidal: 4553 harmonic: 2123 Sorted by residual: dihedral pdb=" C5' A B 61 " pdb=" C4' A B 61 " pdb=" C3' A B 61 " pdb=" O3' A B 61 " ideal model delta sinusoidal sigma weight residual 147.00 98.59 48.41 1 8.00e+00 1.56e-02 5.04e+01 dihedral pdb=" O4' A B 61 " pdb=" C4' A B 61 " pdb=" C3' A B 61 " pdb=" C2' A B 61 " ideal model delta sinusoidal sigma weight residual 24.00 -20.51 44.51 1 8.00e+00 1.56e-02 4.30e+01 dihedral pdb=" C3' A B 61 " pdb=" C4' A B 61 " pdb=" O4' A B 61 " pdb=" C1' A B 61 " ideal model delta sinusoidal sigma weight residual -2.00 39.32 -41.32 1 8.00e+00 1.56e-02 3.73e+01 ... (remaining 6673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1603 0.131 - 0.263: 243 0.263 - 0.394: 0 0.394 - 0.525: 0 0.525 - 0.657: 7 Chirality restraints: 1853 Sorted by residual: chirality pdb=" P DG D 0 " pdb=" OP1 DG D 0 " pdb=" OP2 DG D 0 " pdb=" O5' DG D 0 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DG D -7 " pdb=" OP1 DG D -7 " pdb=" OP2 DG D -7 " pdb=" O5' DG D -7 " both_signs ideal model delta sigma weight residual True 2.35 2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DC C -10 " pdb=" OP1 DC C -10 " pdb=" OP2 DC C -10 " pdb=" O5' DC C -10 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 1850 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 127 " 0.164 9.50e-02 1.11e+02 7.36e-02 3.69e+00 pdb=" NE ARG A 127 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 127 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 127 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 127 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 557 " 0.134 9.50e-02 1.11e+02 6.07e-02 2.92e+00 pdb=" NE ARG A 557 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 557 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 557 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 557 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -11 " 0.009 2.00e-02 2.50e+03 9.39e-03 2.65e+00 pdb=" N9 G B -11 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G B -11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B -11 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B -11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B -11 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G B -11 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G B -11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B -11 " 0.022 2.00e-02 2.50e+03 pdb=" N2 G B -11 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B -11 " -0.021 2.00e-02 2.50e+03 pdb=" C4 G B -11 " -0.002 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 57 2.60 - 3.17: 7466 3.17 - 3.75: 17942 3.75 - 4.32: 26068 4.32 - 4.90: 36417 Nonbonded interactions: 87950 Sorted by model distance: nonbonded pdb=" OP1 C B 109 " pdb="MG MG B 202 " model vdw 2.019 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 305 " model vdw 2.054 2.170 nonbonded pdb="MG MG B 201 " pdb=" O HOH B 303 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 801 " model vdw 2.057 2.170 nonbonded pdb=" OP1 A B 110 " pdb="MG MG B 201 " model vdw 2.062 2.170 ... (remaining 87945 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=0.50 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.011 0.058 10926 Z= 0.654 Angle : 1.490 26.922 15663 Z= 0.938 Chirality : 0.088 0.657 1853 Planarity : 0.005 0.074 1250 Dihedral : 19.136 86.100 5308 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.31 % Allowed : 5.15 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.26), residues: 734 helix: -1.10 (0.26), residues: 283 sheet: -0.45 (0.54), residues: 85 loop : -1.28 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 557 TYR 0.014 0.002 TYR A 543 PHE 0.009 0.002 PHE A 252 TRP 0.008 0.002 TRP A 712 HIS 0.003 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.01074 (10918) covalent geometry : angle 1.46595 (15654) hydrogen bonds : bond 0.18320 ( 458) hydrogen bonds : angle 6.75784 ( 1126) metal coordination : bond 0.02741 ( 8) metal coordination : angle 11.26726 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.321 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 1.0677 time to fit residues: 78.9342 Evaluate side-chains 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 72 ASN A 147 GLN A 156 ASN A 216 GLN A 218 ASN A 220 ASN A 283 ASN A 361 ASN A 486 HIS A 695 ASN A 728 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057210 restraints weight = 33889.337| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.49 r_work: 0.2640 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10926 Z= 0.178 Angle : 0.571 20.828 15663 Z= 0.295 Chirality : 0.035 0.131 1853 Planarity : 0.004 0.034 1250 Dihedral : 20.162 95.342 3729 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.62 % Allowed : 11.39 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.29), residues: 734 helix: 1.28 (0.30), residues: 284 sheet: -0.06 (0.51), residues: 93 loop : -0.37 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 496 TYR 0.010 0.001 TYR A 159 PHE 0.013 0.001 PHE A 635 TRP 0.008 0.001 TRP A 577 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00375 (10918) covalent geometry : angle 0.53778 (15654) hydrogen bonds : bond 0.04303 ( 458) hydrogen bonds : angle 3.68964 ( 1126) metal coordination : bond 0.00886 ( 8) metal coordination : angle 8.00594 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.192 Fit side-chains REVERT: A 24 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7995 (mmt180) REVERT: A 109 MET cc_start: 0.7913 (mtp) cc_final: 0.7421 (ttm) REVERT: A 205 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8822 (tm-30) REVERT: A 423 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8092 (mtm110) REVERT: A 509 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (pp) outliers start: 4 outliers final: 0 residues processed: 44 average time/residue: 0.9027 time to fit residues: 41.6845 Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.055117 restraints weight = 21309.728| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.04 r_work: 0.2581 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10926 Z= 0.334 Angle : 0.606 21.143 15663 Z= 0.309 Chirality : 0.039 0.147 1853 Planarity : 0.004 0.035 1250 Dihedral : 20.334 91.544 3729 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 12.32 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.30), residues: 734 helix: 1.61 (0.31), residues: 287 sheet: 0.08 (0.53), residues: 91 loop : -0.46 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 472 TYR 0.016 0.002 TYR A 543 PHE 0.016 0.002 PHE A 635 TRP 0.015 0.002 TRP A 474 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00709 (10918) covalent geometry : angle 0.57298 (15654) hydrogen bonds : bond 0.04835 ( 458) hydrogen bonds : angle 3.51376 ( 1126) metal coordination : bond 0.01769 ( 8) metal coordination : angle 8.19981 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.241 Fit side-chains REVERT: A 205 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8790 (tm-30) REVERT: A 303 MET cc_start: 0.9137 (mtm) cc_final: 0.8902 (mtp) REVERT: A 423 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8168 (mtm110) REVERT: A 455 ASP cc_start: 0.9384 (t0) cc_final: 0.8913 (t0) REVERT: A 472 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8176 (tmt-80) REVERT: A 509 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 651 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9247 (mppt) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.9680 time to fit residues: 40.7039 Evaluate side-chains 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.055666 restraints weight = 32237.062| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.41 r_work: 0.2594 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10926 Z= 0.214 Angle : 0.538 19.901 15663 Z= 0.276 Chirality : 0.035 0.135 1853 Planarity : 0.004 0.033 1250 Dihedral : 20.316 93.730 3729 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.31 % Allowed : 12.79 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.31), residues: 734 helix: 1.84 (0.31), residues: 287 sheet: 0.05 (0.53), residues: 91 loop : -0.29 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 471 TYR 0.012 0.001 TYR A 697 PHE 0.014 0.002 PHE A 635 TRP 0.010 0.001 TRP A 473 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00450 (10918) covalent geometry : angle 0.50676 (15654) hydrogen bonds : bond 0.04227 ( 458) hydrogen bonds : angle 3.37770 ( 1126) metal coordination : bond 0.01384 ( 8) metal coordination : angle 7.61376 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.314 Fit side-chains REVERT: A 24 ARG cc_start: 0.8322 (mmt180) cc_final: 0.7761 (mpt180) REVERT: A 205 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8764 (tm-30) REVERT: A 455 ASP cc_start: 0.9410 (t0) cc_final: 0.8947 (t0) REVERT: A 472 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8253 (tmt170) REVERT: A 509 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8112 (pp) REVERT: A 651 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9091 (tmmt) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.9930 time to fit residues: 36.5487 Evaluate side-chains 34 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 156 ASN A 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.055290 restraints weight = 40394.302| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.76 r_work: 0.2597 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10926 Z= 0.179 Angle : 0.511 19.258 15663 Z= 0.261 Chirality : 0.033 0.132 1853 Planarity : 0.004 0.034 1250 Dihedral : 20.248 94.535 3729 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.47 % Allowed : 12.95 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.31), residues: 734 helix: 1.97 (0.31), residues: 287 sheet: 0.01 (0.53), residues: 91 loop : -0.26 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.009 0.001 TYR A 697 PHE 0.011 0.001 PHE A 635 TRP 0.007 0.001 TRP A 577 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00378 (10918) covalent geometry : angle 0.47967 (15654) hydrogen bonds : bond 0.03923 ( 458) hydrogen bonds : angle 3.29753 ( 1126) metal coordination : bond 0.01110 ( 8) metal coordination : angle 7.41084 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.244 Fit side-chains REVERT: A 24 ARG cc_start: 0.8296 (mmt180) cc_final: 0.7827 (mpt90) REVERT: A 205 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8753 (tm-30) REVERT: A 455 ASP cc_start: 0.9350 (t0) cc_final: 0.8919 (t0) REVERT: A 472 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8019 (tmt-80) REVERT: A 651 LYS cc_start: 0.9602 (mmmm) cc_final: 0.9319 (mppt) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 1.0521 time to fit residues: 38.6317 Evaluate side-chains 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 472 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.055451 restraints weight = 40290.496| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.77 r_work: 0.2705 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10926 Z= 0.253 Angle : 0.538 18.898 15663 Z= 0.273 Chirality : 0.035 0.135 1853 Planarity : 0.004 0.035 1250 Dihedral : 20.280 93.299 3729 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.47 % Allowed : 13.57 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.31), residues: 734 helix: 1.97 (0.31), residues: 287 sheet: -0.03 (0.53), residues: 91 loop : -0.27 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 423 TYR 0.010 0.001 TYR A 159 PHE 0.012 0.002 PHE A 635 TRP 0.007 0.001 TRP A 577 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00536 (10918) covalent geometry : angle 0.50827 (15654) hydrogen bonds : bond 0.04138 ( 458) hydrogen bonds : angle 3.32283 ( 1126) metal coordination : bond 0.01462 ( 8) metal coordination : angle 7.32953 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.9221 (t0) cc_final: 0.8885 (t0) REVERT: A 472 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8039 (tmt-80) REVERT: A 651 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9313 (mppt) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.9858 time to fit residues: 38.2101 Evaluate side-chains 33 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063533 restraints weight = 27355.877| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.28 r_work: 0.2807 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10926 Z= 0.117 Angle : 0.481 16.980 15663 Z= 0.245 Chirality : 0.031 0.122 1853 Planarity : 0.003 0.035 1250 Dihedral : 20.179 95.482 3729 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.32), residues: 734 helix: 2.18 (0.31), residues: 288 sheet: 0.02 (0.53), residues: 91 loop : -0.17 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.007 0.001 TYR A 30 PHE 0.009 0.001 PHE A 635 TRP 0.009 0.001 TRP A 577 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00246 (10918) covalent geometry : angle 0.45441 (15654) hydrogen bonds : bond 0.03543 ( 458) hydrogen bonds : angle 3.19478 ( 1126) metal coordination : bond 0.00847 ( 8) metal coordination : angle 6.55867 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.252 Fit side-chains REVERT: A 24 ARG cc_start: 0.8419 (mmt180) cc_final: 0.8079 (mpt90) REVERT: A 455 ASP cc_start: 0.9343 (t0) cc_final: 0.8948 (t0) REVERT: A 472 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8110 (tmt-80) REVERT: A 651 LYS cc_start: 0.9525 (mmmm) cc_final: 0.9291 (mppt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.9857 time to fit residues: 35.1991 Evaluate side-chains 31 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063623 restraints weight = 30092.478| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.37 r_work: 0.2816 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10926 Z= 0.130 Angle : 0.471 16.059 15663 Z= 0.240 Chirality : 0.030 0.123 1853 Planarity : 0.003 0.035 1250 Dihedral : 20.132 95.260 3729 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.16 % Allowed : 13.88 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.32), residues: 734 helix: 2.28 (0.31), residues: 287 sheet: -0.21 (0.50), residues: 101 loop : -0.09 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.008 0.001 TYR A 30 PHE 0.009 0.001 PHE A 635 TRP 0.007 0.001 TRP A 577 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00275 (10918) covalent geometry : angle 0.44661 (15654) hydrogen bonds : bond 0.03421 ( 458) hydrogen bonds : angle 3.15089 ( 1126) metal coordination : bond 0.00856 ( 8) metal coordination : angle 6.28901 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.293 Fit side-chains REVERT: A 24 ARG cc_start: 0.8352 (mmt180) cc_final: 0.7831 (mpt90) REVERT: A 455 ASP cc_start: 0.9367 (t0) cc_final: 0.8965 (t0) REVERT: A 472 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8280 (tmt170) REVERT: A 651 LYS cc_start: 0.9502 (mmmm) cc_final: 0.9254 (mppt) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.9417 time to fit residues: 34.6899 Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 0.0020 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062573 restraints weight = 35027.508| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.56 r_work: 0.2772 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10926 Z= 0.164 Angle : 0.489 16.680 15663 Z= 0.249 Chirality : 0.031 0.129 1853 Planarity : 0.003 0.041 1250 Dihedral : 20.126 94.626 3729 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.16 % Allowed : 14.35 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.32), residues: 734 helix: 2.27 (0.31), residues: 287 sheet: -0.07 (0.52), residues: 91 loop : -0.18 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.008 0.001 TYR A 30 PHE 0.010 0.001 PHE A 635 TRP 0.007 0.001 TRP A 441 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00348 (10918) covalent geometry : angle 0.46369 (15654) hydrogen bonds : bond 0.03517 ( 458) hydrogen bonds : angle 3.16280 ( 1126) metal coordination : bond 0.00977 ( 8) metal coordination : angle 6.45727 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.373 Fit side-chains REVERT: A 24 ARG cc_start: 0.8420 (mmt180) cc_final: 0.7926 (mpt90) REVERT: A 455 ASP cc_start: 0.9372 (t0) cc_final: 0.8961 (t0) REVERT: A 472 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8275 (tmt170) REVERT: A 651 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9260 (mppt) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9145 time to fit residues: 36.5587 Evaluate side-chains 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 46 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.063426 restraints weight = 31293.424| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.41 r_work: 0.2799 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10926 Z= 0.118 Angle : 0.477 16.387 15663 Z= 0.243 Chirality : 0.030 0.126 1853 Planarity : 0.003 0.041 1250 Dihedral : 20.142 95.611 3729 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.16 % Allowed : 14.82 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.32), residues: 734 helix: 2.32 (0.31), residues: 287 sheet: -0.08 (0.52), residues: 91 loop : -0.15 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.017 0.001 TYR A 499 PHE 0.014 0.001 PHE A 470 TRP 0.008 0.001 TRP A 577 HIS 0.002 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00248 (10918) covalent geometry : angle 0.45207 (15654) hydrogen bonds : bond 0.03439 ( 458) hydrogen bonds : angle 3.16004 ( 1126) metal coordination : bond 0.00781 ( 8) metal coordination : angle 6.34822 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.260 Fit side-chains REVERT: A 24 ARG cc_start: 0.8386 (mmt180) cc_final: 0.7889 (mpt90) REVERT: A 455 ASP cc_start: 0.9354 (t0) cc_final: 0.8948 (t0) REVERT: A 472 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8257 (tmt170) REVERT: A 651 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9258 (mppt) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.8761 time to fit residues: 33.2587 Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062915 restraints weight = 27533.483| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.27 r_work: 0.2794 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10926 Z= 0.160 Angle : 0.481 16.776 15663 Z= 0.245 Chirality : 0.031 0.130 1853 Planarity : 0.003 0.042 1250 Dihedral : 20.113 94.810 3729 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.31 % Allowed : 14.51 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.32), residues: 734 helix: 2.31 (0.31), residues: 287 sheet: -0.11 (0.52), residues: 91 loop : -0.14 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.008 0.001 TYR A 159 PHE 0.011 0.001 PHE A 635 TRP 0.007 0.001 TRP A 441 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00338 (10918) covalent geometry : angle 0.45505 (15654) hydrogen bonds : bond 0.03499 ( 458) hydrogen bonds : angle 3.15745 ( 1126) metal coordination : bond 0.00972 ( 8) metal coordination : angle 6.47577 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.25 seconds wall clock time: 62 minutes 55.62 seconds (3775.62 seconds total)