Starting phenix.real_space_refine on Fri Sep 11 00:44:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cag_45390/09_2026/9cag_45390_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cag_45390/09_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_45390/09_2026/9cag_45390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cag_45390/09_2026/9cag_45390.map" model { file = "/net/cci-nas-00/data/ceres_data/9cag_45390/09_2026/9cag_45390_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cag_45390/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.66, per 1000 atoms: 0.27 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: 0.64 Conformation dependent library (CDL) restraints added in 405.2 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: 0.69 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: 1.09 Time building geometry restraints manager: 0.68 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 1.20e-02 6.94e+03 4.69e+01 bond pdb=" O3' U E -1 " pdb=" P A E 0 " ideal model delta sigma weight residual 1.607 1.551 0.056 1.20e-02 6.94e+03 2.18e+01 bond pdb=" O3' A E 0 " pdb=" P A E 1 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.20e-02 6.94e+03 2.07e+01 bond pdb=" O3' A E 1 " pdb=" P A E 2 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.20e-02 6.94e+03 1.08e+01 bond pdb=" O3' A E 2 " pdb=" P A E 3 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.20e-02 6.94e+03 1.07e+01 ... (remaining 6368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8537 2.27 - 4.53: 107 4.53 - 6.80: 12 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 2.00e+00 2.50e-01 3.21e+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 2.00e+00 2.50e-01 1.67e+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 angle pdb=" C3' A E 0 " pdb=" C2' A E 0 " pdb=" C1' A E 0 " ideal model delta sigma weight residual 101.30 103.65 -2.35 7.00e-01 2.04e+00 1.12e+01 angle pdb=" O3' A E 2 " pdb=" C3' A E 2 " pdb=" C2' A E 2 " ideal model delta sigma weight residual 113.70 108.39 5.31 1.60e+00 3.91e-01 1.10e+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: 822 0.057 - 0.115: 133 0.115 - 0.172: 16 0.172 - 0.229: 4 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 2.320 nonbonded pdb=" OP1 A E 3 " pdb="MN MN A 702 " model vdw 2.080 2.320 nonbonded pdb=" OE1 GLU A 340 " pdb="MN MN A 701 " model vdw 2.094 2.320 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 702 " model vdw 2.128 2.320 nonbonded pdb=" OE1 GLU A 9 " pdb="MN MN A 702 " model vdw 2.128 2.320 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- 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= 0.237 Angle : 0.623 11.328 8659 Z= 0.348 Chirality : 0.047 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 0.00416 / 0.24 ( 6373) covalent geometry : angle 0.62270 / 0.35 ( 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 : 0.239 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: 0.6586 (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: 0.7146 (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: 0.0938 time to fit residues: 25.0519 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 : 0.264 ------------------------------------------------------------------------------- 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: 0.0050 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: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 382 HIS B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098640 restraints weight = 9836.360| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.09 r_work: 0.3102 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6373 Z= 0.160 Angle : 0.553 6.538 8659 Z= 0.293 Chirality : 0.044 0.219 978 Planarity : 0.004 0.059 1090 Dihedral : 9.047 112.036 934 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.11 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: 0.68 (0.31), residues: 769 helix: 1.24 (0.30), residues: 302 sheet: 0.88 (0.42), residues: 151 loop : -0.48 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.016 0.002 TYR A 41 PHE 0.020 0.002 PHE B 111 TRP 0.014 0.001 TRP A 458 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6373) covalent geometry : angle 0.55255 / 0.29 ( 8659) hydrogen bonds : bond 0.03790 / 2.49 ( 278) hydrogen bonds : angle 4.37291 / 2.98 ( 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 208 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.165 Fit side-chains REVERT: A 15 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7596 (tt0) REVERT: A 65 ASP cc_start: 0.8089 (t0) cc_final: 0.7832 (t0) REVERT: A 126 CYS cc_start: 0.7671 (m) cc_final: 0.7205 (m) REVERT: A 152 PHE cc_start: 0.8290 (p90) cc_final: 0.8058 (p90) REVERT: A 176 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 231 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8306 (ttmm) REVERT: A 235 PHE cc_start: 0.8606 (t80) cc_final: 0.8128 (t80) REVERT: A 256 LEU cc_start: 0.8264 (tp) cc_final: 0.8001 (tp) REVERT: A 386 ASP cc_start: 0.7697 (t0) cc_final: 0.7480 (t0) REVERT: A 424 CYS cc_start: 0.8021 (t) cc_final: 0.7725 (t) REVERT: A 427 LEU cc_start: 0.8518 (tp) cc_final: 0.8311 (tt) REVERT: A 511 ASP cc_start: 0.6853 (p0) cc_final: 0.6634 (p0) REVERT: A 608 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7314 (tm-30) outliers start: 13 outliers final: 9 residues processed: 196 average time/residue: 0.0965 time to fit residues: 24.0012 Evaluate side-chains 201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.0020 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.109505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098778 restraints weight = 9679.697| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.08 r_work: 0.3101 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1033 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= 0.130 Angle : 0.517 6.662 8659 Z= 0.270 Chirality : 0.042 0.186 978 Planarity : 0.004 0.051 1090 Dihedral : 8.801 106.764 934 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 1.65 % Allowed : 14.52 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 769 helix: 1.23 (0.30), residues: 302 sheet: 0.75 (0.42), residues: 157 loop : -0.46 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.018 0.001 TYR A 41 PHE 0.014 0.001 PHE B 111 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 0.00288 / 0.13 ( 6373) covalent geometry : angle 0.51705 / 0.27 ( 8659) hydrogen bonds : bond 0.03454 / 2.28 ( 278) hydrogen bonds : angle 4.25901 / 2.91 ( 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 200 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.238 Fit side-chains REVERT: A 15 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7593 (tt0) REVERT: A 63 THR cc_start: 0.8376 (t) cc_final: 0.8053 (p) REVERT: A 65 ASP cc_start: 0.8109 (t0) cc_final: 0.7847 (t0) REVERT: A 100 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8134 (mtpp) REVERT: A 126 CYS cc_start: 0.7716 (m) cc_final: 0.7295 (m) REVERT: A 152 PHE cc_start: 0.8307 (p90) cc_final: 0.7991 (p90) REVERT: A 231 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8317 (ttmm) REVERT: A 235 PHE cc_start: 0.8613 (t80) cc_final: 0.8134 (t80) REVERT: A 256 LEU cc_start: 0.8209 (tp) cc_final: 0.7995 (tp) REVERT: A 347 ASN cc_start: 0.7969 (p0) cc_final: 0.7689 (p0) REVERT: A 424 CYS cc_start: 0.8002 (t) cc_final: 0.7701 (t) REVERT: A 480 GLU cc_start: 0.7694 (pm20) cc_final: 0.7281 (pm20) REVERT: A 608 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 11 outliers final: 11 residues processed: 189 average time/residue: 0.0939 time to fit residues: 22.5982 Evaluate side-chains 197 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097220 restraints weight = 9688.700| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.09 r_work: 0.3083 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6373 Z= 0.195 Angle : 0.546 7.194 8659 Z= 0.284 Chirality : 0.043 0.185 978 Planarity : 0.004 0.048 1090 Dihedral : 8.713 102.866 934 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.74 % 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: 0.42 (0.31), residues: 769 helix: 1.06 (0.30), residues: 305 sheet: 0.62 (0.41), residues: 157 loop : -0.62 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.019 0.002 TYR A 41 PHE 0.015 0.002 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 0.00444 / 0.20 ( 6373) covalent geometry : angle 0.54632 / 0.28 ( 8659) hydrogen bonds : bond 0.03774 / 2.49 ( 278) hydrogen bonds : angle 4.27911 / 2.92 ( 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 205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.292 Fit side-chains REVERT: A 15 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7606 (tt0) REVERT: A 63 THR cc_start: 0.8452 (t) cc_final: 0.8167 (p) REVERT: A 65 ASP cc_start: 0.8060 (t0) cc_final: 0.7817 (t0) REVERT: A 126 CYS cc_start: 0.7783 (m) cc_final: 0.7328 (m) REVERT: A 231 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8375 (ttmm) REVERT: A 235 PHE cc_start: 0.8635 (t80) cc_final: 0.8141 (t80) REVERT: A 322 MET cc_start: 0.8414 (tpp) cc_final: 0.8149 (mmt) REVERT: A 424 CYS cc_start: 0.8038 (t) cc_final: 0.7719 (t) REVERT: A 440 PHE cc_start: 0.8385 (m-80) cc_final: 0.7940 (m-80) REVERT: A 480 GLU cc_start: 0.7709 (pm20) cc_final: 0.7361 (pm20) REVERT: A 608 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 74 GLN cc_start: 0.8188 (mp10) cc_final: 0.7896 (mp10) REVERT: B 101 ASP cc_start: 0.7705 (p0) cc_final: 0.7446 (p0) outliers start: 16 outliers final: 13 residues processed: 192 average time/residue: 0.0929 time to fit residues: 22.6556 Evaluate side-chains 198 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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: 0.6980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.108940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098077 restraints weight = 9932.250| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.13 r_work: 0.3092 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1251 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= 0.141 Angle : 0.517 7.091 8659 Z= 0.269 Chirality : 0.041 0.175 978 Planarity : 0.004 0.046 1090 Dihedral : 8.742 101.380 934 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.25 % Allowed : 16.92 % Favored : 80.84 % 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: 0.53 (0.31), residues: 769 helix: 1.21 (0.30), residues: 301 sheet: 0.58 (0.41), residues: 157 loop : -0.55 (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 0.011 0.001 PHE A 152 TRP 0.014 0.001 TRP A 458 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6373) covalent geometry : angle 0.51678 / 0.27 ( 8659) hydrogen bonds : bond 0.03494 / 2.30 ( 278) hydrogen bonds : angle 4.21355 / 2.87 ( 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 203 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.217 Fit side-chains REVERT: A 15 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7629 (tt0) REVERT: A 63 THR cc_start: 0.8470 (t) cc_final: 0.8194 (p) REVERT: A 65 ASP cc_start: 0.8055 (t0) cc_final: 0.7807 (t0) REVERT: A 235 PHE cc_start: 0.8635 (t80) cc_final: 0.8140 (t80) REVERT: A 322 MET cc_start: 0.8378 (tpp) cc_final: 0.8129 (mmt) REVERT: A 347 ASN cc_start: 0.8138 (p0) cc_final: 0.7844 (p0) REVERT: A 424 CYS cc_start: 0.8090 (t) cc_final: 0.7771 (t) REVERT: A 440 PHE cc_start: 0.8391 (m-80) cc_final: 0.7968 (m-80) REVERT: A 480 GLU cc_start: 0.7695 (pm20) cc_final: 0.7409 (pm20) REVERT: A 554 GLU cc_start: 0.8122 (tt0) cc_final: 0.7921 (tt0) REVERT: A 608 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7326 (tm-30) REVERT: B 74 GLN cc_start: 0.8216 (mp10) cc_final: 0.7887 (mp10) REVERT: B 101 ASP cc_start: 0.7702 (p0) cc_final: 0.7427 (p0) outliers start: 15 outliers final: 14 residues processed: 191 average time/residue: 0.0878 time to fit residues: 21.1893 Evaluate side-chains 200 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 0.0670 chunk 45 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098384 restraints weight = 9738.403| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.10 r_work: 0.3093 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1335 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= 0.130 Angle : 0.510 7.210 8659 Z= 0.264 Chirality : 0.041 0.171 978 Planarity : 0.004 0.045 1090 Dihedral : 8.677 99.643 934 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 17.37 % Favored : 80.24 % 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: 1.28 (0.30), residues: 301 sheet: 0.58 (0.42), residues: 157 loop : -0.54 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.017 0.001 TYR A 41 PHE 0.019 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6373) covalent geometry : angle 0.50980 / 0.26 ( 8659) hydrogen bonds : bond 0.03375 / 2.22 ( 278) hydrogen bonds : angle 4.14240 / 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 200 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.181 Fit side-chains REVERT: A 15 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7618 (tt0) REVERT: A 63 THR cc_start: 0.8475 (t) cc_final: 0.8202 (p) REVERT: A 65 ASP cc_start: 0.8053 (t0) cc_final: 0.7812 (t0) REVERT: A 126 CYS cc_start: 0.7664 (m) cc_final: 0.7268 (m) REVERT: A 235 PHE cc_start: 0.8621 (t80) cc_final: 0.8140 (t80) REVERT: A 322 MET cc_start: 0.8369 (tpp) cc_final: 0.8121 (mmt) REVERT: A 424 CYS cc_start: 0.8098 (t) cc_final: 0.7754 (t) REVERT: A 440 PHE cc_start: 0.8394 (m-80) cc_final: 0.8005 (m-80) REVERT: A 554 GLU cc_start: 0.8109 (tt0) cc_final: 0.7872 (tt0) REVERT: A 608 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 74 GLN cc_start: 0.8206 (mp10) cc_final: 0.7839 (mp10) outliers start: 16 outliers final: 14 residues processed: 186 average time/residue: 0.0949 time to fit residues: 22.3658 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 : 0.210 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 117 ILE 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: 0.6980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.109277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098486 restraints weight = 9679.473| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.09 r_work: 0.3100 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1384 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= 0.141 Angle : 0.517 7.644 8659 Z= 0.268 Chirality : 0.041 0.173 978 Planarity : 0.004 0.046 1090 Dihedral : 8.659 98.131 934 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.25 % Allowed : 17.96 % 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: 0.57 (0.31), residues: 769 helix: 1.28 (0.30), residues: 301 sheet: 0.55 (0.42), residues: 157 loop : -0.55 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.015 0.001 TYR A 41 PHE 0.022 0.001 PHE A 152 TRP 0.013 0.001 TRP A 458 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6373) covalent geometry : angle 0.51728 / 0.27 ( 8659) hydrogen bonds : bond 0.03414 / 2.26 ( 278) hydrogen bonds : angle 4.13302 / 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 199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.249 Fit side-chains REVERT: A 15 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7616 (tt0) REVERT: A 63 THR cc_start: 0.8489 (t) cc_final: 0.8210 (p) REVERT: A 65 ASP cc_start: 0.8051 (t0) cc_final: 0.7807 (t0) REVERT: A 126 CYS cc_start: 0.7688 (m) cc_final: 0.7285 (m) REVERT: A 235 PHE cc_start: 0.8621 (t80) cc_final: 0.8178 (t80) REVERT: A 271 GLN cc_start: 0.8061 (tp40) cc_final: 0.7851 (tp-100) REVERT: A 322 MET cc_start: 0.8374 (tpp) cc_final: 0.8130 (mmt) REVERT: A 347 ASN cc_start: 0.8182 (p0) cc_final: 0.7866 (p0) REVERT: A 424 CYS cc_start: 0.8092 (t) cc_final: 0.7759 (t) REVERT: A 603 MET cc_start: 0.7849 (mtm) cc_final: 0.7631 (mtp) REVERT: A 608 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 74 GLN cc_start: 0.8213 (mp10) cc_final: 0.7853 (mp10) outliers start: 15 outliers final: 14 residues processed: 186 average time/residue: 0.0977 time to fit residues: 23.0374 Evaluate side-chains 198 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 ILE 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: 0.5980 chunk 17 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.0170 chunk 37 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.0628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101080 restraints weight = 9775.944| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.12 r_work: 0.3137 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6373 Z= 0.093 Angle : 0.497 8.069 8659 Z= 0.255 Chirality : 0.039 0.178 978 Planarity : 0.004 0.043 1090 Dihedral : 8.788 97.176 934 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 1.80 % Allowed : 19.16 % Favored : 79.04 % 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: 0.61 (0.31), residues: 769 helix: 1.38 (0.30), residues: 300 sheet: 0.49 (0.43), residues: 152 loop : -0.52 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.016 0.001 TYR A 411 PHE 0.021 0.001 PHE A 152 TRP 0.010 0.001 TRP A 458 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 ( 6373) covalent geometry : angle 0.49748 / 0.26 ( 8659) hydrogen bonds : bond 0.02887 / 1.91 ( 278) hydrogen bonds : angle 3.99477 / 2.73 ( 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 198 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.254 Fit side-chains REVERT: A 15 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7548 (tt0) REVERT: A 63 THR cc_start: 0.8402 (t) cc_final: 0.8131 (p) REVERT: A 65 ASP cc_start: 0.8048 (t0) cc_final: 0.7796 (t0) REVERT: A 126 CYS cc_start: 0.7652 (m) cc_final: 0.7307 (m) REVERT: A 235 PHE cc_start: 0.8579 (t80) cc_final: 0.8137 (t80) REVERT: A 246 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7808 (ttmm) REVERT: A 424 CYS cc_start: 0.8083 (t) cc_final: 0.7770 (t) REVERT: A 425 LYS cc_start: 0.8410 (mttp) cc_final: 0.8168 (mttm) REVERT: A 480 GLU cc_start: 0.7594 (pm20) cc_final: 0.7214 (pm20) REVERT: A 608 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 74 GLN cc_start: 0.8138 (mp10) cc_final: 0.7811 (mp10) outliers start: 12 outliers final: 7 residues processed: 189 average time/residue: 0.0973 time to fit residues: 23.3148 Evaluate side-chains 191 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 246 LYS 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 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 41 optimal weight: 0.2980 chunk 59 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099864 restraints weight = 9789.997| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.11 r_work: 0.3115 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1607 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= 0.117 Angle : 0.498 7.192 8659 Z= 0.258 Chirality : 0.040 0.211 978 Planarity : 0.004 0.044 1090 Dihedral : 8.698 95.401 934 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.25 % Allowed : 18.41 % Favored : 79.34 % 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: 0.62 (0.31), residues: 769 helix: 1.40 (0.30), residues: 300 sheet: 0.48 (0.43), residues: 152 loop : -0.52 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.013 0.001 TYR A 411 PHE 0.023 0.001 PHE A 152 TRP 0.011 0.001 TRP A 458 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6373) covalent geometry : angle 0.49778 / 0.26 ( 8659) hydrogen bonds : bond 0.03114 / 2.06 ( 278) hydrogen bonds : angle 4.01098 / 2.73 ( 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 203 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.241 Fit side-chains REVERT: A 15 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7580 (tt0) REVERT: A 63 THR cc_start: 0.8455 (t) cc_final: 0.8174 (p) REVERT: A 65 ASP cc_start: 0.8042 (t0) cc_final: 0.7804 (t0) REVERT: A 126 CYS cc_start: 0.7675 (m) cc_final: 0.7289 (m) REVERT: A 235 PHE cc_start: 0.8610 (t80) cc_final: 0.8140 (t80) REVERT: A 340 GLU cc_start: 0.8025 (tt0) cc_final: 0.7539 (mt-10) REVERT: A 424 CYS cc_start: 0.8091 (t) cc_final: 0.7725 (t) REVERT: A 608 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 74 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: B 79 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7469 (m) outliers start: 15 outliers final: 10 residues processed: 191 average time/residue: 0.0937 time to fit residues: 22.7170 Evaluate side-chains 198 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 17 SER 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 10 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.110983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100058 restraints weight = 9747.717| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.10 r_work: 0.3122 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1614 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= 0.114 Angle : 0.508 7.122 8659 Z= 0.261 Chirality : 0.040 0.208 978 Planarity : 0.004 0.044 1090 Dihedral : 8.690 94.531 934 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % 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: 0.66 (0.31), residues: 769 helix: 1.39 (0.30), residues: 299 sheet: 0.52 (0.41), residues: 159 loop : -0.47 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 472 TYR 0.013 0.001 TYR A 411 PHE 0.022 0.001 PHE A 152 TRP 0.012 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6373) covalent geometry : angle 0.50803 / 0.26 ( 8659) hydrogen bonds : bond 0.03134 / 2.08 ( 278) hydrogen bonds : angle 4.01654 / 2.75 ( 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 199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.211 Fit side-chains REVERT: A 15 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7578 (tt0) REVERT: A 63 THR cc_start: 0.8465 (t) cc_final: 0.8167 (p) REVERT: A 65 ASP cc_start: 0.8049 (t0) cc_final: 0.7815 (t0) REVERT: A 126 CYS cc_start: 0.7684 (m) cc_final: 0.7287 (m) REVERT: A 235 PHE cc_start: 0.8593 (t80) cc_final: 0.8124 (t80) REVERT: A 271 GLN cc_start: 0.8005 (tp40) cc_final: 0.7581 (tp-100) REVERT: A 340 GLU cc_start: 0.7976 (tt0) cc_final: 0.7363 (mt-10) REVERT: A 424 CYS cc_start: 0.8076 (t) cc_final: 0.7712 (t) REVERT: A 608 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7186 (tm-30) REVERT: B 74 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: B 79 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7464 (m) outliers start: 13 outliers final: 11 residues processed: 189 average time/residue: 0.0909 time to fit residues: 21.7809 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 : 0.238 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 217 CYS 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 70 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS A 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097579 restraints weight = 9768.412| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.09 r_work: 0.3086 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6373 Z= 0.198 Angle : 0.560 8.633 8659 Z= 0.290 Chirality : 0.043 0.200 978 Planarity : 0.004 0.045 1090 Dihedral : 8.572 91.802 934 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % 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: 0.53 (0.31), residues: 769 helix: 1.25 (0.30), residues: 298 sheet: 0.49 (0.43), residues: 152 loop : -0.50 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 434 TYR 0.014 0.002 TYR A 41 PHE 0.023 0.002 PHE A 152 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 0.00453 / 0.20 ( 6373) covalent geometry : angle 0.56037 / 0.29 ( 8659) hydrogen bonds : bond 0.03812 / 2.54 ( 278) hydrogen bonds : angle 4.15622 / 2.83 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1635.36 seconds wall clock time: 28 minutes 47.64 seconds (1727.64 seconds total)