Starting phenix.real_space_refine on Tue Mar 11 15:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cag_45390/03_2025/9cag_45390_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cag_45390/03_2025/9cag_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_45390/03_2025/9cag_45390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cag_45390/03_2025/9cag_45390.map" model { file = "/net/cci-nas-00/data/ceres_data/9cag_45390/03_2025/9cag_45390_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cag_45390/03_2025/9cag_45390_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.76, per 1000 atoms: 0.76 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: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.09 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: 1.98 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.550 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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= 0.264 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 458 HIS 0.015 0.001 HIS A 172 PHE 0.026 0.002 PHE B 111 TYR 0.012 0.001 TYR A 411 ARG 0.007 0.001 ARG A 579 *********************** 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 : 0.762 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: 0.2154 time to fit residues: 57.0480 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 284 GLN A 347 ASN A 382 HIS B 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097882 restraints weight = 9667.379| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.05 r_work: 0.3096 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0932 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= 0.272 Angle : 0.549 6.541 8659 Z= 0.289 Chirality : 0.044 0.253 978 Planarity : 0.004 0.061 1090 Dihedral : 9.138 114.239 934 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 11.38 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.31), residues: 769 helix: 1.06 (0.30), residues: 306 sheet: 0.81 (0.42), residues: 156 loop : -0.50 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.023 0.002 PHE B 111 TYR 0.016 0.002 TYR A 41 ARG 0.005 0.001 ARG A 579 *********************** 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 207 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.669 Fit side-chains REVERT: A 15 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7612 (tt0) REVERT: A 63 THR cc_start: 0.8356 (t) cc_final: 0.7938 (p) REVERT: A 65 ASP cc_start: 0.8067 (t0) cc_final: 0.7782 (t0) REVERT: A 126 CYS cc_start: 0.7723 (m) cc_final: 0.7256 (m) REVERT: A 176 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7981 (mp) REVERT: A 210 SER cc_start: 0.8744 (p) cc_final: 0.8543 (p) REVERT: A 231 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8358 (ttmm) REVERT: A 235 PHE cc_start: 0.8622 (t80) cc_final: 0.8176 (t80) REVERT: A 347 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7782 (p0) REVERT: A 424 CYS cc_start: 0.8022 (t) cc_final: 0.7741 (t) REVERT: A 480 GLU cc_start: 0.7644 (pm20) cc_final: 0.7200 (pm20) REVERT: A 511 ASP cc_start: 0.6900 (p0) cc_final: 0.6690 (p0) REVERT: A 608 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 13 outliers final: 9 residues processed: 196 average time/residue: 0.2279 time to fit residues: 55.9621 Evaluate side-chains 201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 347 ASN 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 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3364 r_free = 0.3364 target = 0.107883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097210 restraints weight = 9690.201| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.3082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1162 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= 0.294 Angle : 0.543 7.715 8659 Z= 0.285 Chirality : 0.044 0.256 978 Planarity : 0.004 0.054 1090 Dihedral : 8.950 108.776 934 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 2.10 % Allowed : 15.12 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 769 helix: 1.04 (0.30), residues: 305 sheet: 0.72 (0.42), residues: 157 loop : -0.58 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.016 0.002 PHE B 111 TYR 0.017 0.002 TYR A 41 ARG 0.006 0.000 ARG A 579 *********************** 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 205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.658 Fit side-chains REVERT: A 15 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7621 (tt0) REVERT: A 63 THR cc_start: 0.8461 (t) cc_final: 0.8119 (p) REVERT: A 65 ASP cc_start: 0.8034 (t0) cc_final: 0.7801 (t0) REVERT: A 100 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: A 126 CYS cc_start: 0.7773 (m) cc_final: 0.7289 (m) REVERT: A 210 SER cc_start: 0.8745 (p) cc_final: 0.8544 (p) REVERT: A 235 PHE cc_start: 0.8621 (t80) cc_final: 0.8160 (t80) REVERT: A 347 ASN cc_start: 0.8045 (p0) cc_final: 0.7770 (p0) REVERT: A 424 CYS cc_start: 0.8063 (t) cc_final: 0.7723 (t) REVERT: A 440 PHE cc_start: 0.8406 (m-80) cc_final: 0.7932 (m-80) REVERT: A 480 GLU cc_start: 0.7687 (pm20) cc_final: 0.7336 (pm20) REVERT: A 608 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7340 (tm-30) outliers start: 14 outliers final: 12 residues processed: 191 average time/residue: 0.2225 time to fit residues: 53.2516 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 : 0.778 ------------------------------------------------------------------------------- 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 100 LYS Chi-restraints excluded: chain A residue 104 VAL 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 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 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.0770 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098644 restraints weight = 9745.721| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.10 r_work: 0.3105 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6373 Z= 0.168 Angle : 0.500 7.837 8659 Z= 0.259 Chirality : 0.041 0.223 978 Planarity : 0.004 0.049 1090 Dihedral : 8.920 105.751 934 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.69 % Allowed : 15.87 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 769 helix: 1.28 (0.30), residues: 301 sheet: 0.70 (0.41), residues: 157 loop : -0.49 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.012 0.001 PHE A 127 TYR 0.017 0.001 TYR A 41 ARG 0.006 0.000 ARG A 579 *********************** 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 207 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.682 Fit side-chains REVERT: A 15 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7600 (tt0) REVERT: A 63 THR cc_start: 0.8433 (t) cc_final: 0.8109 (p) REVERT: A 65 ASP cc_start: 0.8053 (t0) cc_final: 0.7788 (t0) REVERT: A 100 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: A 152 PHE cc_start: 0.8283 (p90) cc_final: 0.7975 (p90) REVERT: A 176 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 235 PHE cc_start: 0.8612 (t80) cc_final: 0.8173 (t80) REVERT: A 424 CYS cc_start: 0.8062 (t) cc_final: 0.7737 (t) REVERT: A 440 PHE cc_start: 0.8383 (m-80) cc_final: 0.7942 (m-80) REVERT: A 456 MET cc_start: 0.8705 (mtp) cc_final: 0.8491 (mtm) REVERT: A 608 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7261 (tm-30) outliers start: 18 outliers final: 14 residues processed: 192 average time/residue: 0.2217 time to fit residues: 53.4579 Evaluate side-chains 206 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 100 LYS 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 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 Chi-restraints excluded: chain B residue 117 ILE 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 0 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3379 r_free = 0.3379 target = 0.109202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098317 restraints weight = 9733.919| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.10 r_work: 0.3098 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1396 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= 0.199 Angle : 0.503 5.945 8659 Z= 0.261 Chirality : 0.041 0.229 978 Planarity : 0.004 0.047 1090 Dihedral : 8.872 102.971 934 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.25 % Allowed : 17.81 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.31), residues: 769 helix: 1.30 (0.30), residues: 301 sheet: 0.65 (0.41), residues: 157 loop : -0.52 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.011 0.001 PHE A 127 TYR 0.014 0.001 TYR A 41 ARG 0.006 0.000 ARG A 434 *********************** 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 202 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.624 Fit side-chains REVERT: A 15 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7605 (tt0) REVERT: A 57 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 63 THR cc_start: 0.8474 (t) cc_final: 0.8161 (p) REVERT: A 65 ASP cc_start: 0.8040 (t0) cc_final: 0.7757 (t0) REVERT: A 100 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8169 (mtpp) REVERT: A 126 CYS cc_start: 0.7675 (m) cc_final: 0.7292 (m) REVERT: A 152 PHE cc_start: 0.8275 (p90) cc_final: 0.7974 (p90) REVERT: A 235 PHE cc_start: 0.8618 (t80) cc_final: 0.8155 (t80) REVERT: A 322 MET cc_start: 0.8383 (tpp) cc_final: 0.8135 (mmt) REVERT: A 340 GLU cc_start: 0.8061 (tt0) cc_final: 0.7340 (mt-10) REVERT: A 424 CYS cc_start: 0.8080 (t) cc_final: 0.7774 (t) REVERT: A 425 LYS cc_start: 0.8498 (mttp) cc_final: 0.8226 (mttm) REVERT: A 554 GLU cc_start: 0.8031 (tt0) cc_final: 0.7821 (tt0) REVERT: A 608 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 74 GLN cc_start: 0.8161 (mp10) cc_final: 0.7884 (mp10) outliers start: 15 outliers final: 12 residues processed: 190 average time/residue: 0.2345 time to fit residues: 55.6837 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL 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 117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 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 = 0.3368 r_free = 0.3368 target = 0.108410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097577 restraints weight = 9644.740| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.07 r_work: 0.3086 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6373 Z= 0.242 Angle : 0.522 8.237 8659 Z= 0.269 Chirality : 0.042 0.239 978 Planarity : 0.004 0.046 1090 Dihedral : 8.822 100.773 934 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 18.41 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.31), residues: 769 helix: 1.26 (0.30), residues: 300 sheet: 0.61 (0.42), residues: 155 loop : -0.51 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.011 0.001 PHE A 127 TYR 0.013 0.002 TYR A 41 ARG 0.007 0.001 ARG A 579 *********************** 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 : 0.702 Fit side-chains REVERT: A 15 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7618 (tt0) REVERT: A 57 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 63 THR cc_start: 0.8489 (t) cc_final: 0.8180 (p) REVERT: A 65 ASP cc_start: 0.8001 (t0) cc_final: 0.7728 (t0) REVERT: A 100 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8185 (mtpp) REVERT: A 126 CYS cc_start: 0.7714 (m) cc_final: 0.7315 (m) REVERT: A 235 PHE cc_start: 0.8605 (t80) cc_final: 0.8116 (t80) REVERT: A 322 MET cc_start: 0.8418 (tpp) cc_final: 0.8180 (mmt) REVERT: A 340 GLU cc_start: 0.8074 (tt0) cc_final: 0.7471 (mt-10) REVERT: A 424 CYS cc_start: 0.8083 (t) cc_final: 0.7783 (t) REVERT: A 425 LYS cc_start: 0.8510 (mttp) cc_final: 0.8228 (mttm) REVERT: A 554 GLU cc_start: 0.8081 (tt0) cc_final: 0.7860 (tt0) REVERT: A 608 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7245 (tm-30) outliers start: 16 outliers final: 14 residues processed: 187 average time/residue: 0.2378 time to fit residues: 55.8512 Evaluate side-chains 196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.0060 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099208 restraints weight = 9680.843| |-----------------------------------------------------------------------------| 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: 0.2953 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1555 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= 0.165 Angle : 0.494 6.222 8659 Z= 0.255 Chirality : 0.040 0.219 978 Planarity : 0.004 0.046 1090 Dihedral : 8.870 100.110 934 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 2.99 % Allowed : 18.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.31), residues: 769 helix: 1.37 (0.30), residues: 300 sheet: 0.55 (0.41), residues: 158 loop : -0.51 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.022 0.001 PHE A 152 TYR 0.017 0.001 TYR A 41 ARG 0.007 0.000 ARG A 579 *********************** 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 205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.782 Fit side-chains REVERT: A 15 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7572 (tt0) REVERT: A 57 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 63 THR cc_start: 0.8417 (t) cc_final: 0.8131 (p) REVERT: A 65 ASP cc_start: 0.8030 (t0) cc_final: 0.7745 (t0) REVERT: A 126 CYS cc_start: 0.7689 (m) cc_final: 0.7282 (m) REVERT: A 235 PHE cc_start: 0.8601 (t80) cc_final: 0.8138 (t80) REVERT: A 322 MET cc_start: 0.8384 (tpp) cc_final: 0.8134 (mmt) REVERT: A 340 GLU cc_start: 0.8066 (tt0) cc_final: 0.7509 (mt-10) REVERT: A 424 CYS cc_start: 0.8109 (t) cc_final: 0.7792 (t) REVERT: A 425 LYS cc_start: 0.8477 (mttp) cc_final: 0.8207 (mttm) REVERT: A 608 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7196 (tm-30) outliers start: 20 outliers final: 14 residues processed: 191 average time/residue: 0.2452 time to fit residues: 58.5014 Evaluate side-chains 194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 100 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097217 restraints weight = 9734.774| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.07 r_work: 0.3082 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1569 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= 0.290 Angle : 0.535 8.067 8659 Z= 0.279 Chirality : 0.043 0.249 978 Planarity : 0.004 0.046 1090 Dihedral : 8.780 97.091 934 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 18.41 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.31), residues: 769 helix: 1.22 (0.30), residues: 300 sheet: 0.51 (0.42), residues: 152 loop : -0.50 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.022 0.002 PHE A 152 TYR 0.017 0.002 TYR A 41 ARG 0.007 0.001 ARG A 472 *********************** 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 206 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.733 Fit side-chains REVERT: A 15 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7623 (tt0) REVERT: A 57 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 63 THR cc_start: 0.8459 (t) cc_final: 0.8214 (p) REVERT: A 65 ASP cc_start: 0.7984 (t0) cc_final: 0.7728 (t0) REVERT: A 126 CYS cc_start: 0.7784 (m) cc_final: 0.7329 (m) REVERT: A 235 PHE cc_start: 0.8619 (t80) cc_final: 0.8142 (t80) REVERT: A 322 MET cc_start: 0.8432 (tpp) cc_final: 0.8186 (mmt) REVERT: A 340 GLU cc_start: 0.8127 (tt0) cc_final: 0.7729 (mt-10) REVERT: A 424 CYS cc_start: 0.8093 (t) cc_final: 0.7791 (t) REVERT: A 544 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 608 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7345 (tm-30) outliers start: 18 outliers final: 16 residues processed: 193 average time/residue: 0.2239 time to fit residues: 54.4480 Evaluate side-chains 205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 57 VAL 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 398 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 LEU 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 111 PHE 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 66 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096521 restraints weight = 9811.942| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6373 Z= 0.346 Angle : 0.565 8.103 8659 Z= 0.295 Chirality : 0.044 0.263 978 Planarity : 0.004 0.046 1090 Dihedral : 8.732 94.549 934 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 2.69 % Allowed : 19.16 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 769 helix: 1.11 (0.30), residues: 300 sheet: 0.42 (0.42), residues: 151 loop : -0.52 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.022 0.002 PHE A 152 TYR 0.017 0.002 TYR A 41 ARG 0.007 0.001 ARG A 472 *********************** 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 201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.674 Fit side-chains REVERT: A 15 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7654 (tt0) REVERT: A 63 THR cc_start: 0.8489 (t) cc_final: 0.8251 (p) REVERT: A 65 ASP cc_start: 0.7961 (t0) cc_final: 0.7732 (t0) REVERT: A 126 CYS cc_start: 0.7847 (m) cc_final: 0.7394 (m) REVERT: A 235 PHE cc_start: 0.8635 (t80) cc_final: 0.8173 (t80) REVERT: A 322 MET cc_start: 0.8421 (tpp) cc_final: 0.8174 (mmt) REVERT: A 340 GLU cc_start: 0.8135 (tt0) cc_final: 0.7657 (mt-10) REVERT: A 424 CYS cc_start: 0.8164 (t) cc_final: 0.7840 (t) REVERT: A 544 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7905 (mp) REVERT: A 608 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7352 (tm-30) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.2301 time to fit residues: 54.6211 Evaluate side-chains 199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 A residue 544 LEU 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 111 PHE 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 47 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 23 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 0.0010 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098645 restraints weight = 9716.026| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1659 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= 0.189 Angle : 0.516 8.103 8659 Z= 0.267 Chirality : 0.041 0.231 978 Planarity : 0.004 0.045 1090 Dihedral : 8.788 94.853 934 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 769 helix: 1.28 (0.30), residues: 300 sheet: 0.54 (0.43), residues: 152 loop : -0.50 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.023 0.001 PHE A 152 TYR 0.021 0.001 TYR A 41 ARG 0.007 0.000 ARG A 579 ********************** 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 201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.665 Fit side-chains REVERT: A 15 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7597 (tt0) REVERT: A 63 THR cc_start: 0.8417 (t) cc_final: 0.8201 (p) REVERT: A 65 ASP cc_start: 0.8015 (t0) cc_final: 0.7785 (t0) REVERT: A 126 CYS cc_start: 0.7770 (m) cc_final: 0.7299 (m) REVERT: A 235 PHE cc_start: 0.8594 (t80) cc_final: 0.8106 (t80) REVERT: A 322 MET cc_start: 0.8399 (tpp) cc_final: 0.8168 (mmt) REVERT: A 340 GLU cc_start: 0.8148 (tt0) cc_final: 0.7683 (mt-10) REVERT: A 424 CYS cc_start: 0.8115 (t) cc_final: 0.7788 (t) REVERT: A 608 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7312 (tm-30) outliers start: 15 outliers final: 13 residues processed: 191 average time/residue: 0.2236 time to fit residues: 53.6364 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 : 0.730 ------------------------------------------------------------------------------- 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 70 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 PHE 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 20 optimal weight: 0.0370 chunk 76 optimal weight: 0.0000 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099563 restraints weight = 9844.051| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.12 r_work: 0.3112 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1761 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= 0.156 Angle : 0.505 5.609 8659 Z= 0.262 Chirality : 0.040 0.221 978 Planarity : 0.004 0.045 1090 Dihedral : 8.847 93.542 934 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.95 % Allowed : 20.51 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 769 helix: 1.37 (0.31), residues: 300 sheet: 0.56 (0.43), residues: 152 loop : -0.48 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 458 HIS 0.006 0.001 HIS A 382 PHE 0.022 0.001 PHE A 152 TYR 0.019 0.001 TYR A 41 ARG 0.007 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.38 seconds wall clock time: 61 minutes 5.79 seconds (3665.79 seconds total)