Starting phenix.real_space_refine on Wed Aug 5 15:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k32_62004/08_2026/9k32_62004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k32_62004/08_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_62004/08_2026/9k32_62004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k32_62004/08_2026/9k32_62004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k32_62004/08_2026/9k32_62004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k32_62004/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.73, per 1000 atoms: 0.26 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: 0.69 Conformation dependent library (CDL) restraints added in 455.4 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: 1.70 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: 3.02 Time building geometry restraints manager: 0.97 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: 13274 1.98 - 3.96: 2115 3.96 - 5.94: 240 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=" C4' A B 61 " pdb=" O4' A B 61 " pdb=" C1' A B 61 " ideal model delta sigma weight residual 109.70 106.15 3.55 7.00e-01 2.04e+00 2.57e+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: 1683 0.133 - 0.267: 163 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- 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= 0.726 Angle : 1.452 26.922 15663 Z= 0.996 Chirality : 0.082 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 0.01087 / 0.73 (10918) covalent geometry : angle 1.42716 / 0.99 (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 : 0.219 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 1.0720 time to fit residues: 79.4850 Evaluate side-chains 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 1.9990 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: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 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 = 0.3369 r_free = 0.3369 target = 0.086906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057327 restraints weight = 34090.189| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.49 r_work: 0.2643 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- 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: 0.8757 moved from start: 0.1707 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= 0.157 Angle : 0.622 23.502 15663 Z= 0.346 Chirality : 0.039 0.183 1853 Planarity : 0.004 0.030 1250 Dihedral : 20.208 93.669 3729 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.71 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: 0.97 (0.30), residues: 285 sheet: -0.15 (0.50), residues: 93 loop : -0.47 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00291 / 0.16 (10918) covalent geometry : angle 0.58533 / 0.34 (15654) hydrogen bonds : bond 0.05911 / 3.99 ( 458) hydrogen bonds : angle 4.05608 / 2.83 ( 1126) metal coordination : bond 0.00891 / 0.46 ( 8) metal coordination : angle 8.76974 / 3.96 ( 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 42 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8741 (tm-30) REVERT: A 455 ASP cc_start: 0.9264 (t0) cc_final: 0.8715 (t0) REVERT: A 472 ARG cc_start: 0.8430 (tmt-80) cc_final: 0.8032 (tmt-80) REVERT: A 509 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8098 (pp) outliers start: 4 outliers final: 0 residues processed: 40 average time/residue: 0.7915 time to fit residues: 33.3910 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 : 0.279 ------------------------------------------------------------------------------- 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: 30.0000 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.055586 restraints weight = 21072.976| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.02 r_work: 0.2602 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 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 = 0.2488 r_free = 0.2488 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 (9 function evaluations) r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10926 Z= 0.279 Angle : 0.643 21.404 15663 Z= 0.343 Chirality : 0.044 0.212 1853 Planarity : 0.005 0.036 1250 Dihedral : 20.284 92.687 3729 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 11.54 % Favored : 88.14 % 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: 0.48 (0.30), residues: 734 helix: 1.40 (0.31), residues: 288 sheet: 0.05 (0.53), residues: 91 loop : -0.47 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 160 TYR 0.016 0.002 TYR A 543 PHE 0.014 0.002 PHE A 252 TRP 0.051 0.003 TRP A 473 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.28 (10918) covalent geometry : angle 0.61134 / 0.34 (15654) hydrogen bonds : bond 0.05556 / 3.81 ( 458) hydrogen bonds : angle 3.63562 / 2.55 ( 1126) metal coordination : bond 0.01749 / 0.80 ( 8) metal coordination : angle 8.29427 / 3.71 ( 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 41 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8815 (tm-30) REVERT: A 455 ASP cc_start: 0.9386 (t0) cc_final: 0.8834 (t0) REVERT: A 509 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8158 (pp) REVERT: A 651 LYS cc_start: 0.9561 (mmmm) cc_final: 0.9091 (tmmt) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.8543 time to fit residues: 36.0912 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 : 0.285 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057367 restraints weight = 32050.144| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.44 r_work: 0.2644 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 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 = 0.2525 r_free = 0.2525 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: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2392 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= 0.135 Angle : 0.503 19.334 15663 Z= 0.283 Chirality : 0.034 0.160 1853 Planarity : 0.003 0.031 1250 Dihedral : 20.300 94.513 3729 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.16 % Allowed : 12.64 % Favored : 87.21 % 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: 0.88 (0.31), residues: 734 helix: 1.87 (0.31), residues: 285 sheet: -0.02 (0.52), residues: 93 loop : -0.27 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 655 TYR 0.008 0.001 TYR A 697 PHE 0.013 0.001 PHE A 635 TRP 0.016 0.002 TRP A 473 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (10918) covalent geometry : angle 0.47140 / 0.28 (15654) hydrogen bonds : bond 0.04653 / 3.18 ( 458) hydrogen bonds : angle 3.43666 / 2.39 ( 1126) metal coordination : bond 0.00912 / 0.40 ( 8) metal coordination : angle 7.39009 / 3.32 ( 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 40 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.287 Fit side-chains REVERT: A 3 LYS cc_start: 0.9197 (mppt) cc_final: 0.8868 (mmmt) REVERT: A 24 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8098 (mmt180) REVERT: A 205 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8774 (tm-30) REVERT: A 455 ASP cc_start: 0.9417 (t0) cc_final: 0.8894 (t0) REVERT: A 509 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 651 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9067 (tmmt) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.9138 time to fit residues: 37.7876 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 : 0.289 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.085500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.055739 restraints weight = 40176.882| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.71 r_work: 0.2582 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10926 Z= 0.209 Angle : 0.533 19.118 15663 Z= 0.291 Chirality : 0.038 0.158 1853 Planarity : 0.004 0.036 1250 Dihedral : 20.280 93.302 3729 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 13.42 % Favored : 86.27 % 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: 0.85 (0.31), residues: 734 helix: 1.87 (0.31), residues: 289 sheet: 0.04 (0.53), residues: 91 loop : -0.35 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.012 0.001 TYR A 159 PHE 0.012 0.002 PHE A 635 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (10918) covalent geometry : angle 0.50298 / 0.29 (15654) hydrogen bonds : bond 0.04779 / 3.27 ( 458) hydrogen bonds : angle 3.40018 / 2.37 ( 1126) metal coordination : bond 0.01386 / 0.65 ( 8) metal coordination : angle 7.35160 / 3.30 ( 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 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8914 (ttmm) REVERT: A 205 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8739 (tm-30) REVERT: A 455 ASP cc_start: 0.9353 (t0) cc_final: 0.8864 (t0) REVERT: A 509 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (pp) REVERT: A 651 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9298 (mppt) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.8128 time to fit residues: 30.8415 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS 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: 8.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.056702 restraints weight = 40135.753| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.72 r_work: 0.2625 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 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: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2547 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= 0.135 Angle : 0.487 18.001 15663 Z= 0.274 Chirality : 0.035 0.162 1853 Planarity : 0.004 0.103 1250 Dihedral : 20.313 94.390 3729 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.31 % Allowed : 13.57 % 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: 0.99 (0.31), residues: 734 helix: 2.00 (0.31), residues: 288 sheet: 0.04 (0.53), residues: 91 loop : -0.25 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 472 TYR 0.008 0.001 TYR A 697 PHE 0.012 0.001 PHE A 635 TRP 0.022 0.002 TRP A 473 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (10918) covalent geometry : angle 0.45867 / 0.27 (15654) hydrogen bonds : bond 0.04484 / 3.06 ( 458) hydrogen bonds : angle 3.34832 / 2.33 ( 1126) metal coordination : bond 0.00895 / 0.42 ( 8) metal coordination : angle 6.88203 / 3.07 ( 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 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8766 (tm-30) REVERT: A 455 ASP cc_start: 0.9338 (t0) cc_final: 0.8867 (t0) REVERT: A 509 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8051 (pp) REVERT: A 651 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9302 (mppt) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.9283 time to fit residues: 34.3803 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 chunk 17 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058551 restraints weight = 24515.663| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.15 r_work: 0.2678 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10926 Z= 0.117 Angle : 0.470 17.648 15663 Z= 0.267 Chirality : 0.033 0.158 1853 Planarity : 0.004 0.074 1250 Dihedral : 20.298 94.771 3729 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.47 % Allowed : 14.20 % Favored : 85.34 % 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 (0.31), residues: 734 helix: 2.06 (0.31), residues: 288 sheet: 0.04 (0.52), residues: 91 loop : -0.21 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.007 0.001 TYR A 697 PHE 0.011 0.001 PHE A 635 TRP 0.024 0.003 TRP A 473 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (10918) covalent geometry : angle 0.44143 / 0.27 (15654) hydrogen bonds : bond 0.04373 / 2.99 ( 458) hydrogen bonds : angle 3.30966 / 2.29 ( 1126) metal coordination : bond 0.00709 / 0.36 ( 8) metal coordination : angle 6.75648 / 3.01 ( 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 36 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8361 (mmt180) cc_final: 0.8150 (mmt180) REVERT: A 205 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8810 (tm-30) REVERT: A 455 ASP cc_start: 0.9400 (t0) cc_final: 0.8915 (t0) REVERT: A 509 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 651 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9287 (mppt) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.9705 time to fit residues: 34.7791 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 : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 472 ARG 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: 4.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.087031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.058035 restraints weight = 27430.530| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.31 r_work: 0.2664 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 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: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10926 Z= 0.140 Angle : 0.470 17.297 15663 Z= 0.264 Chirality : 0.034 0.157 1853 Planarity : 0.004 0.043 1250 Dihedral : 20.278 94.360 3729 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.62 % Allowed : 14.35 % 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: 1.09 (0.31), residues: 734 helix: 2.10 (0.31), residues: 288 sheet: 0.01 (0.52), residues: 91 loop : -0.19 (0.33), residues: 355 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 0.010 0.001 PHE A 635 TRP 0.009 0.001 TRP A 473 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (10918) covalent geometry : angle 0.44249 / 0.26 (15654) hydrogen bonds : bond 0.04311 / 2.95 ( 458) hydrogen bonds : angle 3.27477 / 2.26 ( 1126) metal coordination : bond 0.01026 / 0.49 ( 8) metal coordination : angle 6.64861 / 2.98 ( 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: 4 poor density : 34 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8809 (tm-30) REVERT: A 455 ASP cc_start: 0.9399 (t0) cc_final: 0.8876 (t0) REVERT: A 651 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9293 (mppt) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.8213 time to fit residues: 30.3733 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 : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 472 ARG 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: 0.0570 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 10.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.057286 restraints weight = 31856.479| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.43 r_work: 0.2641 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10926 Z= 0.170 Angle : 0.488 17.219 15663 Z= 0.269 Chirality : 0.035 0.156 1853 Planarity : 0.004 0.037 1250 Dihedral : 20.303 93.959 3729 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.47 % Allowed : 14.35 % 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: 1.08 (0.31), residues: 734 helix: 2.08 (0.31), residues: 288 sheet: 0.04 (0.53), residues: 91 loop : -0.20 (0.33), residues: 355 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 0.010 0.001 PHE A 635 TRP 0.009 0.001 TRP A 473 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (10918) covalent geometry : angle 0.46232 / 0.27 (15654) hydrogen bonds : bond 0.04358 / 2.98 ( 458) hydrogen bonds : angle 3.27706 / 2.27 ( 1126) metal coordination : bond 0.01130 / 0.53 ( 8) metal coordination : angle 6.58035 / 2.95 ( 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 37 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8777 (tm-30) REVERT: A 455 ASP cc_start: 0.9407 (t0) cc_final: 0.8857 (t0) REVERT: A 651 LYS cc_start: 0.9605 (mmmm) cc_final: 0.9072 (tmmt) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.7788 time to fit residues: 28.8689 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 472 ARG 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: 10.0000 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.057063 restraints weight = 24822.433| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.18 r_work: 0.2644 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 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: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10926 Z= 0.189 Angle : 0.514 17.769 15663 Z= 0.280 Chirality : 0.036 0.156 1853 Planarity : 0.004 0.042 1250 Dihedral : 20.333 93.494 3729 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.06 (0.31), residues: 734 helix: 2.08 (0.31), residues: 288 sheet: -0.00 (0.53), residues: 91 loop : -0.21 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 224 TYR 0.010 0.001 TYR A 159 PHE 0.010 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 0.00380 / 0.19 (10918) covalent geometry : angle 0.48648 / 0.28 (15654) hydrogen bonds : bond 0.04458 / 3.05 ( 458) hydrogen bonds : angle 3.29472 / 2.29 ( 1126) metal coordination : bond 0.01272 / 0.60 ( 8) metal coordination : angle 6.89495 / 3.12 ( 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 34 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8370 (mmt180) cc_final: 0.7768 (mpt90) REVERT: A 205 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8779 (tm-30) REVERT: A 455 ASP cc_start: 0.9365 (t0) cc_final: 0.8831 (t0) REVERT: A 651 LYS cc_start: 0.9580 (mmmm) cc_final: 0.9281 (mppt) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.9249 time to fit residues: 33.2361 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 : 0.277 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.0470 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 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: 0.6980 chunk 50 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.057919 restraints weight = 23873.583| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.15 r_work: 0.2668 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 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 = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10926 Z= 0.122 Angle : 0.482 17.416 15663 Z= 0.268 Chirality : 0.033 0.159 1853 Planarity : 0.004 0.039 1250 Dihedral : 20.360 94.626 3729 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.31 % Allowed : 14.82 % Favored : 84.87 % 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: 1.13 (0.31), residues: 734 helix: 2.14 (0.31), residues: 288 sheet: 0.00 (0.53), residues: 91 loop : -0.16 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 224 TYR 0.008 0.001 TYR A 159 PHE 0.010 0.001 PHE A 635 TRP 0.008 0.001 TRP A 577 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (10918) covalent geometry : angle 0.45416 / 0.27 (15654) hydrogen bonds : bond 0.04327 / 2.96 ( 458) hydrogen bonds : angle 3.26893 / 2.26 ( 1126) metal coordination : bond 0.00867 / 0.40 ( 8) metal coordination : angle 6.72057 / 3.01 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.39 seconds wall clock time: 57 minutes 20.49 seconds (3440.49 seconds total)