Starting phenix.real_space_refine on Thu Jul 2 21:30:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k32_62004/07_2026/9k32_62004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k32_62004/07_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_62004/07_2026/9k32_62004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k32_62004/07_2026/9k32_62004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k32_62004/07_2026/9k32_62004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k32_62004/07_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-6108/lib/python3.11/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: 2.96, per 1000 atoms: 0.29 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: 0.89 Conformation dependent library (CDL) restraints added in 470.1 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: 1.22 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: 2.55 Time building geometry restraints manager: 1.15 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=" P DG D -7 " pdb=" O5' DG D -7 " ideal model delta sigma weight residual 1.593 1.626 -0.033 1.00e-02 1.00e+04 1.06e+01 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13063 1.98 - 3.96: 2323 3.96 - 5.94: 243 5.94 - 7.92: 24 7.92 - 9.90: 1 Bond angle restraints: 15654 Sorted by residual: angle pdb=" O4' DG D 2 " pdb=" C1' DG D 2 " pdb=" N9 DG D 2 " ideal model delta sigma weight residual 108.00 112.49 -4.49 7.00e-01 2.04e+00 4.11e+01 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 ... (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 - 0.133: 1606 0.133 - 0.267: 240 0.267 - 0.400: 0 0.400 - 0.534: 0 0.534 - 0.667: 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 2.34 -3.00 -0.67 2.00e-01 2.50e+01 1.11e+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 2.34 2.99 -0.66 2.00e-01 2.50e+01 1.08e+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 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+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: 0.770 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.060 Find NCS groups from input model: 0.030 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:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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= 0.713 Angle : 1.492 26.922 15663 Z= 1.008 Chirality : 0.090 0.667 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/Z covalent geometry : bond 0.01093 / 0.71 (10918) covalent geometry : angle 1.46797 / 1.01 (15654) hydrogen bonds : bond 0.18320 / 12.12 ( 458) hydrogen bonds : angle 6.75784 / 4.81 ( 1126) metal coordination : bond 0.02741 / 1.23 ( 8) metal coordination : angle 11.26726 / 5.14 ( 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 : 0.206 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.8901 time to fit residues: 65.9542 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 : 0.232 ------------------------------------------------------------------------------- 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: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 57 GLN A 72 ASN A 147 GLN A 216 GLN A 218 ASN A 220 ASN A 283 ASN A 361 ASN ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 728 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057066 restraints weight = 34168.863| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.50 r_work: 0.2624 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10926 Z= 0.181 Angle : 0.614 23.350 15663 Z= 0.346 Chirality : 0.039 0.162 1853 Planarity : 0.004 0.030 1250 Dihedral : 20.243 94.089 3729 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.62 % Allowed : 11.86 % Favored : 87.52 % 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: 0.15 (0.29), residues: 734 helix: 0.98 (0.30), residues: 285 sheet: -0.14 (0.50), residues: 93 loop : -0.48 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 496 TYR 0.012 0.002 TYR A 543 PHE 0.014 0.002 PHE A 635 TRP 0.008 0.001 TRP A 577 HIS 0.003 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (10918) covalent geometry : angle 0.57763 / 0.34 (15654) hydrogen bonds : bond 0.05665 / 3.82 ( 458) hydrogen bonds : angle 4.00622 / 2.79 ( 1126) metal coordination : bond 0.00952 / 0.48 ( 8) metal coordination : angle 8.70045 / 3.93 ( 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 43 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8747 (tm-30) REVERT: A 455 ASP cc_start: 0.9276 (t0) cc_final: 0.8736 (t0) REVERT: A 509 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (pp) outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.7314 time to fit residues: 31.5090 Evaluate side-chains 34 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 486 HIS A 524 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.054858 restraints weight = 21239.338| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.11 r_work: 0.2596 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 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 = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10926 Z= 0.337 Angle : 0.630 21.784 15663 Z= 0.349 Chirality : 0.042 0.180 1853 Planarity : 0.005 0.042 1250 Dihedral : 20.273 91.053 3729 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.31 % Allowed : 11.86 % Favored : 87.83 % 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: 0.38 (0.30), residues: 734 helix: 1.35 (0.31), residues: 288 sheet: 0.05 (0.53), residues: 91 loop : -0.56 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 347 TYR 0.017 0.002 TYR A 543 PHE 0.013 0.002 PHE A 252 TRP 0.010 0.002 TRP A 577 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.34 (10918) covalent geometry : angle 0.59602 / 0.35 (15654) hydrogen bonds : bond 0.05720 / 3.89 ( 458) hydrogen bonds : angle 3.67951 / 2.59 ( 1126) metal coordination : bond 0.02051 / 0.95 ( 8) metal coordination : angle 8.47979 / 3.83 ( 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 40 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8806 (tm-30) REVERT: A 455 ASP cc_start: 0.9384 (t0) cc_final: 0.8836 (t0) REVERT: A 509 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8175 (pp) REVERT: A 651 LYS cc_start: 0.9567 (mmmm) cc_final: 0.9118 (tmmt) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.8170 time to fit residues: 33.3237 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 715 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.055959 restraints weight = 32501.006| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.47 r_work: 0.2608 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10926 Z= 0.209 Angle : 0.524 20.003 15663 Z= 0.296 Chirality : 0.036 0.162 1853 Planarity : 0.004 0.036 1250 Dihedral : 20.367 93.558 3729 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.16 % Allowed : 12.79 % Favored : 87.05 % 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: 0.68 (0.31), residues: 734 helix: 1.72 (0.31), residues: 285 sheet: -0.07 (0.52), residues: 93 loop : -0.42 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 655 TYR 0.010 0.001 TYR A 697 PHE 0.014 0.002 PHE A 635 TRP 0.010 0.001 TRP A 473 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 (10918) covalent geometry : angle 0.49095 / 0.29 (15654) hydrogen bonds : bond 0.04778 / 3.24 ( 458) hydrogen bonds : angle 3.48917 / 2.44 ( 1126) metal coordination : bond 0.01287 / 0.60 ( 8) metal coordination : angle 7.66886 / 3.45 ( 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 39 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8519 (mmt180) cc_final: 0.8013 (mpt180) REVERT: A 205 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8787 (tm-30) REVERT: A 455 ASP cc_start: 0.9400 (t0) cc_final: 0.8882 (t0) REVERT: A 509 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 651 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9082 (tmmt) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.8330 time to fit residues: 33.2564 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 184 ASN A 524 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.056433 restraints weight = 40557.322| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.71 r_work: 0.2617 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 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 = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10926 Z= 0.164 Angle : 0.484 18.834 15663 Z= 0.275 Chirality : 0.034 0.159 1853 Planarity : 0.004 0.034 1250 Dihedral : 20.344 94.086 3729 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.62 % Allowed : 12.79 % 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: 0.92 (0.31), residues: 734 helix: 1.89 (0.31), residues: 287 sheet: 0.02 (0.53), residues: 91 loop : -0.24 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 655 TYR 0.008 0.001 TYR A 159 PHE 0.013 0.001 PHE A 635 TRP 0.017 0.002 TRP A 473 HIS 0.003 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (10918) covalent geometry : angle 0.45154 / 0.27 (15654) hydrogen bonds : bond 0.04460 / 3.05 ( 458) hydrogen bonds : angle 3.37759 / 2.34 ( 1126) metal coordination : bond 0.01120 / 0.50 ( 8) metal coordination : angle 7.26560 / 3.27 ( 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 42 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8927 (ttmm) REVERT: A 455 ASP cc_start: 0.9309 (t0) cc_final: 0.8817 (t0) REVERT: A 509 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 651 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9302 (mppt) outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 0.7826 time to fit residues: 32.2314 Evaluate side-chains 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.055737 restraints weight = 40182.678| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.74 r_work: 0.2606 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 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 = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10926 Z= 0.188 Angle : 0.491 18.487 15663 Z= 0.278 Chirality : 0.035 0.160 1853 Planarity : 0.004 0.035 1250 Dihedral : 20.358 93.342 3729 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.62 % Allowed : 13.26 % Favored : 86.12 % 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: 1.92 (0.31), residues: 288 sheet: -0.02 (0.53), residues: 91 loop : -0.22 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.010 0.001 TYR A 159 PHE 0.012 0.001 PHE A 635 TRP 0.009 0.001 TRP A 473 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (10918) covalent geometry : angle 0.46099 / 0.28 (15654) hydrogen bonds : bond 0.04468 / 3.05 ( 458) hydrogen bonds : angle 3.36172 / 2.33 ( 1126) metal coordination : bond 0.01224 / 0.57 ( 8) metal coordination : angle 7.12183 / 3.20 ( 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 39 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8940 (ttmm) REVERT: A 303 MET cc_start: 0.8878 (mtp) cc_final: 0.8520 (mtm) REVERT: A 455 ASP cc_start: 0.9294 (t0) cc_final: 0.8812 (t0) REVERT: A 509 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8202 (pp) REVERT: A 651 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9311 (mppt) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.8064 time to fit residues: 31.3549 Evaluate side-chains 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057227 restraints weight = 24598.074| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.14 r_work: 0.2645 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10926 Z= 0.160 Angle : 0.477 17.986 15663 Z= 0.271 Chirality : 0.034 0.159 1853 Planarity : 0.003 0.034 1250 Dihedral : 20.379 94.099 3729 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.02 (0.31), residues: 734 helix: 2.00 (0.31), residues: 287 sheet: 0.02 (0.53), residues: 91 loop : -0.20 (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 159 PHE 0.011 0.001 PHE A 635 TRP 0.007 0.001 TRP A 577 HIS 0.006 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (10918) covalent geometry : angle 0.44750 / 0.27 (15654) hydrogen bonds : bond 0.04380 / 2.98 ( 458) hydrogen bonds : angle 3.33275 / 2.30 ( 1126) metal coordination : bond 0.01045 / 0.49 ( 8) metal coordination : angle 6.91842 / 3.10 ( 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 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.252 Fit side-chains REVERT: A 24 ARG cc_start: 0.8364 (mmt180) cc_final: 0.8150 (mmt180) REVERT: A 68 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9025 (ttmm) REVERT: A 303 MET cc_start: 0.9039 (mtp) cc_final: 0.8692 (mtm) REVERT: A 455 ASP cc_start: 0.9335 (t0) cc_final: 0.8861 (t0) REVERT: A 509 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 651 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9092 (tmmt) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.8231 time to fit residues: 32.0613 Evaluate side-chains 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057345 restraints weight = 27405.216| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.29 r_work: 0.2654 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10926 Z= 0.153 Angle : 0.470 17.628 15663 Z= 0.267 Chirality : 0.033 0.156 1853 Planarity : 0.004 0.062 1250 Dihedral : 20.377 94.130 3729 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.47 % Allowed : 14.04 % 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: 1.05 (0.31), residues: 734 helix: 2.02 (0.31), residues: 287 sheet: 0.01 (0.53), residues: 91 loop : -0.16 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 224 TYR 0.008 0.001 TYR A 159 PHE 0.012 0.001 PHE A 470 TRP 0.027 0.002 TRP A 473 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (10918) covalent geometry : angle 0.44088 / 0.27 (15654) hydrogen bonds : bond 0.04264 / 2.91 ( 458) hydrogen bonds : angle 3.30829 / 2.28 ( 1126) metal coordination : bond 0.00988 / 0.46 ( 8) metal coordination : angle 6.79338 / 3.05 ( 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 38 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8364 (mmt180) cc_final: 0.7862 (mpt180) REVERT: A 68 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8980 (ttmm) REVERT: A 455 ASP cc_start: 0.9386 (t0) cc_final: 0.8848 (t0) REVERT: A 651 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9299 (mppt) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.9830 time to fit residues: 38.4149 Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS 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: 0.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.055809 restraints weight = 31978.126| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.50 r_work: 0.2605 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- 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 = 0.34 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10926 Z= 0.218 Angle : 0.500 18.369 15663 Z= 0.279 Chirality : 0.035 0.155 1853 Planarity : 0.004 0.038 1250 Dihedral : 20.363 92.896 3729 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.97 (0.31), residues: 734 helix: 1.96 (0.31), residues: 287 sheet: -0.06 (0.53), residues: 91 loop : -0.20 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.012 0.001 TYR A 159 PHE 0.011 0.002 PHE A 635 TRP 0.009 0.001 TRP A 473 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (10918) covalent geometry : angle 0.47080 / 0.28 (15654) hydrogen bonds : bond 0.04517 / 3.09 ( 458) hydrogen bonds : angle 3.33428 / 2.31 ( 1126) metal coordination : bond 0.01430 / 0.68 ( 8) metal coordination : angle 7.09786 / 3.19 ( 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 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8372 (mmt180) cc_final: 0.7991 (mmt90) REVERT: A 68 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8990 (ttmm) REVERT: A 455 ASP cc_start: 0.9394 (t0) cc_final: 0.8858 (t0) REVERT: A 651 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9278 (mppt) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.8471 time to fit residues: 32.1920 Evaluate side-chains 34 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.057905 restraints weight = 24989.523| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.18 r_work: 0.2664 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10926 Z= 0.131 Angle : 0.468 17.500 15663 Z= 0.264 Chirality : 0.033 0.155 1853 Planarity : 0.004 0.043 1250 Dihedral : 20.365 94.821 3729 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.31 % Allowed : 14.20 % 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: 1.09 (0.31), residues: 734 helix: 2.08 (0.31), residues: 286 sheet: -0.04 (0.53), residues: 91 loop : -0.15 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.008 0.001 TYR A 697 PHE 0.011 0.001 PHE A 635 TRP 0.008 0.001 TRP A 473 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (10918) covalent geometry : angle 0.43867 / 0.26 (15654) hydrogen bonds : bond 0.04173 / 2.85 ( 458) hydrogen bonds : angle 3.28125 / 2.26 ( 1126) metal coordination : bond 0.00953 / 0.45 ( 8) metal coordination : angle 6.77586 / 3.05 ( 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 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8997 (ttmm) REVERT: A 455 ASP cc_start: 0.9366 (t0) cc_final: 0.8840 (t0) REVERT: A 651 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9267 (mppt) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.9338 time to fit residues: 34.5060 Evaluate side-chains 35 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS 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: 0.2980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057450 restraints weight = 24067.408| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.14 r_work: 0.2652 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10926 Z= 0.167 Angle : 0.475 17.709 15663 Z= 0.267 Chirality : 0.034 0.152 1853 Planarity : 0.004 0.040 1250 Dihedral : 20.312 93.722 3729 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 14.20 % 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: 1.06 (0.32), residues: 734 helix: 2.07 (0.31), residues: 287 sheet: -0.10 (0.53), residues: 91 loop : -0.17 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.010 0.001 TYR A 159 PHE 0.011 0.001 PHE A 635 TRP 0.008 0.001 TRP A 473 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (10918) covalent geometry : angle 0.44569 / 0.26 (15654) hydrogen bonds : bond 0.04258 / 2.91 ( 458) hydrogen bonds : angle 3.27819 / 2.26 ( 1126) metal coordination : bond 0.01178 / 0.55 ( 8) metal coordination : angle 6.83978 / 3.08 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3088.98 seconds wall clock time: 53 minutes 20.76 seconds (3200.76 seconds total)