Starting phenix.real_space_refine on Thu Jul 2 03:08:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390.map" model { file = "/net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cag_45390/07_2026/9cag_45390_neut.cif" } resolution = 3.33 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 8 5.49 5 S 39 5.16 5 C 3906 2.51 5 N 1077 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 6231 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4840 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 1.46, per 1000 atoms: 0.23 Number of scatterers: 6231 At special positions: 0 Unit cell: (73.04, 86.32, 133.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 39 16.00 P 8 15.00 O 1199 8.00 N 1077 7.00 C 3906 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: 0.50 Conformation dependent library (CDL) restraints added in 333.5 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 44.1% alpha, 16.3% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.560A pdb=" N ASN A 71 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TRP A 73 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 75 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 76 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.888A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.805A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 203 No H-bonds generated for 'chain 'A' and resid 202 through 203' Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.536A pdb=" N LEU A 207 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.629A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.707A pdb=" N VAL A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.903A pdb=" N ALA A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 557 removed outlier: 4.049A pdb=" N LEU A 557 " --> pdb=" O GLU A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 557' Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.915A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.975A pdb=" N VAL A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.602A pdb=" N ILE B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.519A pdb=" N GLY B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.951A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476 removed outlier: 5.700A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER A 443 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LEU A 256 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N LYS A 445 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 15.883A pdb=" N SER A 254 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 243 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 480 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN A 248 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL A 478 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 142 removed outlier: 9.603A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 110 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 77 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 75 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 100 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 73 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.62 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: 2015 1.34 - 1.46: 918 1.46 - 1.57: 3369 1.57 - 1.69: 10 1.69 - 1.81: 61 Bond restraints: 6373 Sorted by residual: bond pdb=" O3' A E 3 " pdb=" P U E 4 " ideal model delta sigma weight residual 1.607 1.525 0.082 1.50e-02 4.44e+03 3.00e+01 bond pdb=" O3' U E -1 " pdb=" P A E 0 " ideal model delta sigma weight residual 1.607 1.551 0.056 1.50e-02 4.44e+03 1.39e+01 bond pdb=" O3' A E 0 " pdb=" P A E 1 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.50e-02 4.44e+03 1.32e+01 bond pdb=" O3' A E 1 " pdb=" P A E 2 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.50e-02 4.44e+03 6.94e+00 bond pdb=" O3' A E 2 " pdb=" P A E 3 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.84e+00 ... (remaining 6368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8531 2.27 - 4.53: 114 4.53 - 6.80: 11 6.80 - 9.06: 2 9.06 - 11.33: 1 Bond angle restraints: 8659 Sorted by residual: angle pdb=" C4' A E 0 " pdb=" C3' A E 0 " pdb=" O3' A E 0 " ideal model delta sigma weight residual 113.00 101.67 11.33 1.50e+00 4.44e-01 5.70e+01 angle pdb=" C4' A E 1 " pdb=" C3' A E 1 " pdb=" O3' A E 1 " ideal model delta sigma weight residual 113.00 104.83 8.17 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 113.00 106.51 6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" C4' C E -2 " pdb=" C3' C E -2 " pdb=" O3' C E -2 " ideal model delta sigma weight residual 113.00 106.84 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" N ILE A 125 " pdb=" CA ILE A 125 " pdb=" C ILE A 125 " ideal model delta sigma weight residual 111.09 106.13 4.96 1.25e+00 6.40e-01 1.57e+01 ... (remaining 8654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 3602 24.18 - 48.36: 234 48.36 - 72.55: 21 72.55 - 96.73: 6 96.73 - 120.91: 1 Dihedral angle restraints: 3864 sinusoidal: 1630 harmonic: 2234 Sorted by residual: dihedral pdb=" O4' A E 1 " pdb=" C2' A E 1 " pdb=" C1' A E 1 " pdb=" C3' A E 1 " ideal model delta sinusoidal sigma weight residual 25.00 -8.95 33.95 1 8.00e+00 1.56e-02 2.56e+01 dihedral pdb=" C4' A E 1 " pdb=" O4' A E 1 " pdb=" C1' A E 1 " pdb=" C2' A E 1 " ideal model delta sinusoidal sigma weight residual 3.00 -30.89 33.89 1 8.00e+00 1.56e-02 2.55e+01 dihedral pdb=" O4' A E 0 " pdb=" C2' A E 0 " pdb=" C1' A E 0 " pdb=" C3' A E 0 " ideal model delta sinusoidal sigma weight residual 25.00 -8.12 33.12 1 8.00e+00 1.56e-02 2.44e+01 ... (remaining 3861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 816 0.057 - 0.115: 135 0.115 - 0.172: 19 0.172 - 0.229: 5 0.229 - 0.286: 3 Chirality restraints: 978 Sorted by residual: chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' A E 1 " pdb=" C4' A E 1 " pdb=" O3' A E 1 " pdb=" C2' A E 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' A E 0 " pdb=" C4' A E 0 " pdb=" O3' A E 0 " pdb=" C2' A E 0 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 975 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 27 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO B 28 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 0 " 0.021 2.00e-02 2.50e+03 1.08e-02 3.20e+00 pdb=" N9 A E 0 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A E 0 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A E 0 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A E 0 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 0 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A E 0 " -0.000 2.00e-02 2.50e+03 pdb=" N1 A E 0 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A E 0 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A E 0 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A E 0 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 172 " 0.013 2.00e-02 2.50e+03 1.41e-02 3.00e+00 pdb=" CG HIS A 172 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS A 172 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 172 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 172 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 172 " 0.004 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 69 2.63 - 3.20: 5390 3.20 - 3.76: 9386 3.76 - 4.33: 12685 4.33 - 4.90: 21354 Nonbonded interactions: 48884 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 701 " model vdw 2.063 3.060 nonbonded pdb=" OP1 A E 3 " pdb="MN MN A 702 " model vdw 2.080 3.060 nonbonded pdb=" OE1 GLU A 340 " pdb="MN MN A 701 " model vdw 2.094 3.060 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 702 " model vdw 2.128 3.060 nonbonded pdb=" OE1 GLU A 9 " pdb="MN MN A 702 " model vdw 2.128 3.060 ... (remaining 48879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.020 Set scattering table: 0.040 Process input model: 7.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.004 0.082 6373 Z= 0.213 Angle : 0.627 11.328 8659 Z= 0.356 Chirality : 0.048 0.286 978 Planarity : 0.005 0.083 1090 Dihedral : 15.051 120.912 2422 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % 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: 0.57 (0.31), residues: 769 helix: 1.12 (0.30), residues: 302 sheet: 0.67 (0.42), residues: 148 loop : -0.39 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 579 TYR 0.012 0.001 TYR A 411 PHE 0.026 0.002 PHE B 111 TRP 0.016 0.002 TRP A 458 HIS 0.015 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 ( 6373) covalent geometry : angle 0.62687 / 0.36 ( 8659) hydrogen bonds : bond 0.07546 / 5.21 ( 278) hydrogen bonds : angle 4.81983 / 3.27 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.150 Fit side-chains REVERT: A 15 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7339 (tt0) REVERT: A 65 ASP cc_start: 0.7595 (t0) cc_final: 0.7253 (t0) REVERT: A 126 CYS cc_start: 0.7009 (m) cc_final: 0.6587 (m) REVERT: A 231 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7933 (ttmm) REVERT: A 235 PHE cc_start: 0.8454 (t80) cc_final: 0.7908 (t80) REVERT: A 424 CYS cc_start: 0.7402 (t) cc_final: 0.7111 (t) REVERT: A 608 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7147 (tm-30) REVERT: B 135 ILE cc_start: 0.8227 (tt) cc_final: 0.7966 (tt) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.0856 time to fit residues: 22.8053 Evaluate side-chains 196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN A 347 ASN A 382 HIS B 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098455 restraints weight = 9814.960| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.09 r_work: 0.3100 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6373 Z= 0.183 Angle : 0.556 6.561 8659 Z= 0.296 Chirality : 0.044 0.303 978 Planarity : 0.004 0.060 1090 Dihedral : 9.287 117.510 934 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.95 % Allowed : 12.28 % Favored : 85.78 % 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: 0.57 (0.31), residues: 769 helix: 1.10 (0.30), residues: 306 sheet: 0.78 (0.42), residues: 157 loop : -0.51 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.016 0.002 TYR A 41 PHE 0.020 0.002 PHE B 111 TRP 0.015 0.001 TRP A 458 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6373) covalent geometry : angle 0.55639 / 0.30 ( 8659) hydrogen bonds : bond 0.03934 / 2.60 ( 278) hydrogen bonds : angle 4.39593 / 2.99 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.248 Fit side-chains REVERT: A 15 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7612 (tt0) REVERT: A 65 ASP cc_start: 0.8086 (t0) cc_final: 0.7826 (t0) REVERT: A 126 CYS cc_start: 0.7711 (m) cc_final: 0.7253 (m) REVERT: A 152 PHE cc_start: 0.8277 (p90) cc_final: 0.8048 (p90) REVERT: A 176 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 231 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8314 (ttmm) REVERT: A 235 PHE cc_start: 0.8612 (t80) cc_final: 0.8176 (t80) REVERT: A 256 LEU cc_start: 0.8273 (tp) cc_final: 0.8068 (tp) REVERT: A 386 ASP cc_start: 0.7740 (t0) cc_final: 0.7528 (t0) REVERT: A 424 CYS cc_start: 0.8024 (t) cc_final: 0.7696 (t) REVERT: A 427 LEU cc_start: 0.8511 (tp) cc_final: 0.8302 (tt) REVERT: A 608 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7307 (tm-30) outliers start: 13 outliers final: 9 residues processed: 193 average time/residue: 0.0908 time to fit residues: 22.0859 Evaluate side-chains 200 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098988 restraints weight = 9649.493| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.09 r_work: 0.3107 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6373 Z= 0.124 Angle : 0.512 6.419 8659 Z= 0.267 Chirality : 0.042 0.246 978 Planarity : 0.004 0.052 1090 Dihedral : 9.030 112.159 934 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.95 % Allowed : 14.52 % Favored : 83.53 % 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: 0.67 (0.31), residues: 769 helix: 1.25 (0.30), residues: 302 sheet: 0.74 (0.41), residues: 157 loop : -0.46 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.018 0.001 TYR A 41 PHE 0.015 0.001 PHE B 111 TRP 0.012 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6373) covalent geometry : angle 0.51207 / 0.27 ( 8659) hydrogen bonds : bond 0.03426 / 2.25 ( 278) hydrogen bonds : angle 4.25525 / 2.90 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.203 Fit side-chains REVERT: A 15 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7594 (tt0) REVERT: A 63 THR cc_start: 0.8380 (t) cc_final: 0.8058 (p) REVERT: A 65 ASP cc_start: 0.8123 (t0) cc_final: 0.7847 (t0) REVERT: A 100 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8164 (mtpp) REVERT: A 126 CYS cc_start: 0.7730 (m) cc_final: 0.7292 (m) REVERT: A 152 PHE cc_start: 0.8306 (p90) cc_final: 0.7993 (p90) REVERT: A 176 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 231 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8314 (ttmm) REVERT: A 235 PHE cc_start: 0.8610 (t80) cc_final: 0.8135 (t80) REVERT: A 347 ASN cc_start: 0.7960 (p0) cc_final: 0.7688 (p0) REVERT: A 424 CYS cc_start: 0.8038 (t) cc_final: 0.7734 (t) REVERT: A 480 GLU cc_start: 0.7694 (pm20) cc_final: 0.7286 (pm20) REVERT: A 608 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 13 outliers final: 11 residues processed: 188 average time/residue: 0.0940 time to fit residues: 22.3823 Evaluate side-chains 197 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 135 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097262 restraints weight = 9691.411| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.3082 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6373 Z= 0.225 Angle : 0.556 7.277 8659 Z= 0.290 Chirality : 0.044 0.271 978 Planarity : 0.004 0.049 1090 Dihedral : 8.938 108.429 934 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 2.40 % Allowed : 15.42 % Favored : 82.19 % 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: 0.41 (0.31), residues: 769 helix: 1.03 (0.30), residues: 305 sheet: 0.63 (0.41), residues: 157 loop : -0.63 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.017 0.002 TYR A 41 PHE 0.016 0.002 PHE B 111 TRP 0.016 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 6373) covalent geometry : angle 0.55556 / 0.29 ( 8659) hydrogen bonds : bond 0.03902 / 2.59 ( 278) hydrogen bonds : angle 4.30122 / 2.93 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.239 Fit side-chains REVERT: A 15 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7613 (tt0) REVERT: A 63 THR cc_start: 0.8473 (t) cc_final: 0.8178 (p) REVERT: A 65 ASP cc_start: 0.8052 (t0) cc_final: 0.7795 (t0) REVERT: A 100 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8182 (mtpp) REVERT: A 126 CYS cc_start: 0.7790 (m) cc_final: 0.7351 (m) REVERT: A 152 PHE cc_start: 0.8288 (p90) cc_final: 0.7974 (p90) REVERT: A 231 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8371 (ttmm) REVERT: A 235 PHE cc_start: 0.8629 (t80) cc_final: 0.8136 (t80) REVERT: A 322 MET cc_start: 0.8420 (tpp) cc_final: 0.8163 (mmt) REVERT: A 424 CYS cc_start: 0.8091 (t) cc_final: 0.7735 (t) REVERT: A 440 PHE cc_start: 0.8391 (m-80) cc_final: 0.7941 (m-80) REVERT: A 480 GLU cc_start: 0.7715 (pm20) cc_final: 0.7383 (pm20) REVERT: A 608 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7329 (tm-30) REVERT: B 74 GLN cc_start: 0.8209 (mp10) cc_final: 0.7879 (mp10) REVERT: B 101 ASP cc_start: 0.7719 (p0) cc_final: 0.7459 (p0) outliers start: 16 outliers final: 13 residues processed: 190 average time/residue: 0.0924 time to fit residues: 22.2608 Evaluate side-chains 195 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 135 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 22 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097738 restraints weight = 9937.366| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.12 r_work: 0.3088 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6373 Z= 0.162 Angle : 0.527 7.039 8659 Z= 0.275 Chirality : 0.043 0.280 978 Planarity : 0.004 0.047 1090 Dihedral : 8.967 106.985 934 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.25 % Allowed : 17.07 % Favored : 80.69 % 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 (0.31), residues: 769 helix: 1.14 (0.30), residues: 301 sheet: 0.58 (0.41), residues: 157 loop : -0.56 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.018 0.002 TYR A 41 PHE 0.013 0.001 PHE B 111 TRP 0.015 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 6373) covalent geometry : angle 0.52673 / 0.27 ( 8659) hydrogen bonds : bond 0.03657 / 2.42 ( 278) hydrogen bonds : angle 4.24910 / 2.90 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.244 Fit side-chains REVERT: A 15 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7608 (tt0) REVERT: A 63 THR cc_start: 0.8492 (t) cc_final: 0.8213 (p) REVERT: A 65 ASP cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: A 100 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8169 (mtpp) REVERT: A 235 PHE cc_start: 0.8641 (t80) cc_final: 0.8145 (t80) REVERT: A 322 MET cc_start: 0.8398 (tpp) cc_final: 0.8145 (mmt) REVERT: A 347 ASN cc_start: 0.8158 (p0) cc_final: 0.7861 (p0) REVERT: A 424 CYS cc_start: 0.8129 (t) cc_final: 0.7779 (t) REVERT: A 440 PHE cc_start: 0.8392 (m-80) cc_final: 0.7964 (m-80) REVERT: A 480 GLU cc_start: 0.7672 (pm20) cc_final: 0.7392 (pm20) REVERT: A 608 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 74 GLN cc_start: 0.8228 (mp10) cc_final: 0.7872 (mp10) REVERT: B 101 ASP cc_start: 0.7715 (p0) cc_final: 0.7434 (p0) outliers start: 15 outliers final: 14 residues processed: 196 average time/residue: 0.0810 time to fit residues: 20.2620 Evaluate side-chains 199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 135 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 72 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098628 restraints weight = 9725.481| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.10 r_work: 0.3101 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6373 Z= 0.128 Angle : 0.512 7.384 8659 Z= 0.266 Chirality : 0.041 0.242 978 Planarity : 0.004 0.045 1090 Dihedral : 8.914 105.301 934 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.95 % Allowed : 18.26 % Favored : 79.79 % 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: 0.58 (0.31), residues: 769 helix: 1.26 (0.30), residues: 301 sheet: 0.58 (0.42), residues: 157 loop : -0.51 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.018 0.001 TYR A 41 PHE 0.012 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6373) covalent geometry : angle 0.51194 / 0.27 ( 8659) hydrogen bonds : bond 0.03403 / 2.25 ( 278) hydrogen bonds : angle 4.16219 / 2.83 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.216 Fit side-chains REVERT: A 15 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7621 (tt0) REVERT: A 63 THR cc_start: 0.8499 (t) cc_final: 0.8225 (p) REVERT: A 65 ASP cc_start: 0.8059 (t0) cc_final: 0.7810 (t0) REVERT: A 100 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8150 (mtpp) REVERT: A 126 CYS cc_start: 0.7684 (m) cc_final: 0.7287 (m) REVERT: A 235 PHE cc_start: 0.8622 (t80) cc_final: 0.8166 (t80) REVERT: A 322 MET cc_start: 0.8362 (tpp) cc_final: 0.8118 (mmt) REVERT: A 424 CYS cc_start: 0.8077 (t) cc_final: 0.7721 (t) REVERT: A 440 PHE cc_start: 0.8372 (m-80) cc_final: 0.7968 (m-80) REVERT: A 608 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 74 GLN cc_start: 0.8196 (mp10) cc_final: 0.7847 (mp10) outliers start: 13 outliers final: 12 residues processed: 184 average time/residue: 0.0864 time to fit residues: 20.2148 Evaluate side-chains 192 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 135 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099157 restraints weight = 9654.519| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.09 r_work: 0.3109 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6373 Z= 0.118 Angle : 0.507 7.606 8659 Z= 0.263 Chirality : 0.041 0.237 978 Planarity : 0.004 0.051 1090 Dihedral : 8.898 103.742 934 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.95 % Allowed : 19.31 % Favored : 78.74 % 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: 0.57 (0.31), residues: 769 helix: 1.30 (0.30), residues: 301 sheet: 0.52 (0.43), residues: 152 loop : -0.53 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.016 0.001 TYR A 41 PHE 0.022 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6373) covalent geometry : angle 0.50666 / 0.26 ( 8659) hydrogen bonds : bond 0.03290 / 2.17 ( 278) hydrogen bonds : angle 4.11802 / 2.81 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.220 Fit side-chains REVERT: A 15 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7594 (tt0) REVERT: A 63 THR cc_start: 0.8455 (t) cc_final: 0.8187 (p) REVERT: A 65 ASP cc_start: 0.8066 (t0) cc_final: 0.7810 (t0) REVERT: A 100 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8152 (mtpp) REVERT: A 126 CYS cc_start: 0.7675 (m) cc_final: 0.7257 (m) REVERT: A 235 PHE cc_start: 0.8615 (t80) cc_final: 0.8165 (t80) REVERT: A 322 MET cc_start: 0.8359 (tpp) cc_final: 0.8116 (mmt) REVERT: A 347 ASN cc_start: 0.8173 (p0) cc_final: 0.7834 (p0) REVERT: A 424 CYS cc_start: 0.8084 (t) cc_final: 0.7726 (t) REVERT: A 440 PHE cc_start: 0.8396 (m-80) cc_final: 0.8004 (m-80) REVERT: A 554 GLU cc_start: 0.8047 (tt0) cc_final: 0.7842 (tt0) REVERT: A 608 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 74 GLN cc_start: 0.8190 (mp10) cc_final: 0.7829 (mp10) outliers start: 13 outliers final: 12 residues processed: 185 average time/residue: 0.0831 time to fit residues: 19.5169 Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.0050 chunk 74 optimal weight: 0.9980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100339 restraints weight = 9770.567| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.12 r_work: 0.3124 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6373 Z= 0.096 Angle : 0.494 8.141 8659 Z= 0.254 Chirality : 0.040 0.210 978 Planarity : 0.004 0.044 1090 Dihedral : 8.894 102.437 934 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 1.95 % Allowed : 19.46 % Favored : 78.59 % 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: 0.65 (0.31), residues: 769 helix: 1.41 (0.30), residues: 301 sheet: 0.46 (0.43), residues: 152 loop : -0.47 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.015 0.001 TYR A 411 PHE 0.022 0.001 PHE A 152 TRP 0.011 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 6373) covalent geometry : angle 0.49372 / 0.25 ( 8659) hydrogen bonds : bond 0.03019 / 1.98 ( 278) hydrogen bonds : angle 4.02199 / 2.74 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.145 Fit side-chains REVERT: A 15 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7569 (tt0) REVERT: A 63 THR cc_start: 0.8425 (t) cc_final: 0.8152 (p) REVERT: A 65 ASP cc_start: 0.8052 (t0) cc_final: 0.7788 (t0) REVERT: A 100 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8149 (mtpp) REVERT: A 126 CYS cc_start: 0.7692 (m) cc_final: 0.7331 (m) REVERT: A 235 PHE cc_start: 0.8600 (t80) cc_final: 0.8143 (t80) REVERT: A 271 GLN cc_start: 0.8007 (tp40) cc_final: 0.7805 (tp-100) REVERT: A 424 CYS cc_start: 0.8084 (t) cc_final: 0.7719 (t) REVERT: A 434 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8289 (ttm-80) REVERT: A 554 GLU cc_start: 0.8049 (tt0) cc_final: 0.7811 (tt0) REVERT: A 608 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 74 GLN cc_start: 0.8160 (mp10) cc_final: 0.7809 (mp10) REVERT: B 79 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7461 (m) outliers start: 13 outliers final: 10 residues processed: 189 average time/residue: 0.0913 time to fit residues: 21.7458 Evaluate side-chains 196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN A 382 HIS A 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099175 restraints weight = 9789.805| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.10 r_work: 0.3103 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6373 Z= 0.140 Angle : 0.505 7.163 8659 Z= 0.264 Chirality : 0.041 0.230 978 Planarity : 0.004 0.044 1090 Dihedral : 8.841 100.782 934 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.25 % Allowed : 19.31 % Favored : 78.44 % 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: 0.60 (0.31), residues: 769 helix: 1.36 (0.30), residues: 301 sheet: 0.42 (0.43), residues: 152 loop : -0.48 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.013 0.001 TYR A 41 PHE 0.023 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6373) covalent geometry : angle 0.50524 / 0.26 ( 8659) hydrogen bonds : bond 0.03303 / 2.18 ( 278) hydrogen bonds : angle 4.05070 / 2.76 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.225 Fit side-chains REVERT: A 15 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7580 (tt0) REVERT: A 63 THR cc_start: 0.8494 (t) cc_final: 0.8212 (p) REVERT: A 65 ASP cc_start: 0.8056 (t0) cc_final: 0.7804 (t0) REVERT: A 100 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8158 (mtpp) REVERT: A 126 CYS cc_start: 0.7694 (m) cc_final: 0.7281 (m) REVERT: A 235 PHE cc_start: 0.8604 (t80) cc_final: 0.8123 (t80) REVERT: A 271 GLN cc_start: 0.8037 (tp40) cc_final: 0.7816 (tp-100) REVERT: A 340 GLU cc_start: 0.7956 (tt0) cc_final: 0.7286 (mt-10) REVERT: A 424 CYS cc_start: 0.8108 (t) cc_final: 0.7735 (t) REVERT: A 554 GLU cc_start: 0.8054 (tt0) cc_final: 0.7852 (tt0) REVERT: A 608 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 74 GLN cc_start: 0.8187 (mp10) cc_final: 0.7803 (mp10) outliers start: 15 outliers final: 14 residues processed: 185 average time/residue: 0.0914 time to fit residues: 21.3538 Evaluate side-chains 196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 69 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100037 restraints weight = 9710.234| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.10 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6373 Z= 0.107 Angle : 0.504 7.154 8659 Z= 0.260 Chirality : 0.040 0.219 978 Planarity : 0.004 0.044 1090 Dihedral : 8.862 100.279 934 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.10 % Allowed : 19.61 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.31), residues: 769 helix: 1.39 (0.30), residues: 300 sheet: 0.41 (0.43), residues: 152 loop : -0.46 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.014 0.001 TYR A 411 PHE 0.022 0.001 PHE A 152 TRP 0.012 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6373) covalent geometry : angle 0.50434 / 0.26 ( 8659) hydrogen bonds : bond 0.03152 / 2.09 ( 278) hydrogen bonds : angle 4.01344 / 2.74 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.248 Fit side-chains REVERT: A 15 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7565 (tt0) REVERT: A 63 THR cc_start: 0.8422 (t) cc_final: 0.8145 (p) REVERT: A 65 ASP cc_start: 0.8048 (t0) cc_final: 0.7794 (t0) REVERT: A 100 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8154 (mtpp) REVERT: A 126 CYS cc_start: 0.7681 (m) cc_final: 0.7325 (m) REVERT: A 235 PHE cc_start: 0.8608 (t80) cc_final: 0.8157 (t80) REVERT: A 271 GLN cc_start: 0.7992 (tp40) cc_final: 0.7772 (tp-100) REVERT: A 334 ILE cc_start: 0.8258 (mm) cc_final: 0.7517 (pt) REVERT: A 340 GLU cc_start: 0.7984 (tt0) cc_final: 0.7333 (mt-10) REVERT: A 424 CYS cc_start: 0.8110 (t) cc_final: 0.7720 (t) REVERT: A 554 GLU cc_start: 0.8050 (tt0) cc_final: 0.7830 (tt0) REVERT: A 608 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 74 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7797 (mp10) outliers start: 14 outliers final: 13 residues processed: 182 average time/residue: 0.0934 time to fit residues: 21.5934 Evaluate side-chains 194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099103 restraints weight = 9723.163| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.09 r_work: 0.3102 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6373 Z= 0.143 Angle : 0.510 6.968 8659 Z= 0.266 Chirality : 0.041 0.229 978 Planarity : 0.004 0.045 1090 Dihedral : 8.799 98.786 934 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 19.46 % Favored : 78.29 % 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: 0.58 (0.31), residues: 769 helix: 1.31 (0.30), residues: 300 sheet: 0.45 (0.44), residues: 145 loop : -0.45 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.013 0.001 TYR A 41 PHE 0.023 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6373) covalent geometry : angle 0.51017 / 0.27 ( 8659) hydrogen bonds : bond 0.03376 / 2.24 ( 278) hydrogen bonds : angle 4.03559 / 2.75 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.91 seconds wall clock time: 28 minutes 18.51 seconds (1698.51 seconds total)