Starting phenix.real_space_refine on Fri Sep 11 00:28:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.map" model { file = "/net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w8a_65741/09_2026/9w8a_65741.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.076 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3686 2.51 5 N 1018 2.21 5 O 1123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 5865 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4874 Classifications: {'peptide': 626} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 577} Chain breaks: 1 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Time building chain proxies: 1.50, per 1000 atoms: 0.26 Number of scatterers: 5865 At special positions: 0 Unit cell: (63.024, 92.112, 149.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1123 8.00 N 1018 7.00 C 3686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 0.42 Conformation dependent library (CDL) restraints added in 471.7 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 22 sheets defined 5.8% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.565A pdb=" N ASN A 72 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 73 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 75 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.903A pdb=" N LYS A 541 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.672A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 103 removed outlier: 8.716A pdb=" N LEU A 99 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 101 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 27.600A pdb=" N LYS A 112 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 22.773A pdb=" N ASP A 136 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 16.723A pdb=" N GLN A 114 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 13.622A pdb=" N TYR A 134 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N SER A 116 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N LEU A 132 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 11.539A pdb=" N GLN A 118 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N THR A 130 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 120 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 103 removed outlier: 8.716A pdb=" N LEU A 99 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 101 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS A 164 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 117 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N MET A 162 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ILE A 119 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N GLY A 160 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 15.502A pdb=" N ILE A 121 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 18.559A pdb=" N ILE A 158 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151 removed outlier: 4.038A pdb=" N GLU A 174 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 218 Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA8, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA9, first strand: chain 'A' and resid 380 through 385 removed outlier: 3.539A pdb=" N THR A 340 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AB2, first strand: chain 'A' and resid 428 through 434 Processing sheet with id=AB3, first strand: chain 'A' and resid 441 through 445 removed outlier: 3.884A pdb=" N MET A 453 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET A 457 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 562 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU A 459 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 560 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 441 through 445 removed outlier: 3.884A pdb=" N MET A 453 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 472 through 475 removed outlier: 3.607A pdb=" N TYR A 472 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB7, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB8, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AB9, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AC1, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AC2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.500A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.602A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS B 96 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TRP B 119 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 98 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.602A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 123 " --> pdb=" O TYR B 94 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1930 1.34 - 1.46: 1432 1.46 - 1.58: 2609 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 6023 Sorted by residual: bond pdb=" CB PRO A 512 " pdb=" CG PRO A 512 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.79e+00 bond pdb=" CG PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" C ARG A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.05e-01 bond pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 1.464 1.456 0.008 9.30e-03 1.16e+04 6.69e-01 bond pdb=" C VAL A 657 " pdb=" O VAL A 657 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.67e-01 ... (remaining 6018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8134 2.27 - 4.54: 69 4.54 - 6.82: 4 6.82 - 9.09: 1 9.09 - 11.36: 1 Bond angle restraints: 8209 Sorted by residual: angle pdb=" CA PRO A 512 " pdb=" N PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 112.00 106.87 5.13 1.40e+00 5.10e-01 1.34e+01 angle pdb=" CA LEU A 313 " pdb=" CB LEU A 313 " pdb=" CG LEU A 313 " ideal model delta sigma weight residual 116.30 127.66 -11.36 3.50e+00 8.16e-02 1.05e+01 angle pdb=" N GLY A 88 " pdb=" CA GLY A 88 " pdb=" C GLY A 88 " ideal model delta sigma weight residual 113.18 107.48 5.70 2.37e+00 1.78e-01 5.79e+00 angle pdb=" CA PRO A 79 " pdb=" C PRO A 79 " pdb=" N TYR A 80 " ideal model delta sigma weight residual 115.12 117.87 -2.75 1.25e+00 6.40e-01 4.83e+00 angle pdb=" N ASN A 346 " pdb=" CA ASN A 346 " pdb=" CB ASN A 346 " ideal model delta sigma weight residual 113.65 110.54 3.11 1.47e+00 4.63e-01 4.47e+00 ... (remaining 8204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 3184 15.33 - 30.65: 328 30.65 - 45.98: 84 45.98 - 61.31: 15 61.31 - 76.63: 3 Dihedral angle restraints: 3614 sinusoidal: 1427 harmonic: 2187 Sorted by residual: dihedral pdb=" CB CYS A 685 " pdb=" SG CYS A 685 " pdb=" SG CYS A 697 " pdb=" CB CYS A 697 " ideal model delta sinusoidal sigma weight residual 93.00 129.64 -36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual -86.00 -120.58 34.58 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS A 84 " pdb=" SG CYS A 84 " pdb=" SG CYS A 190 " pdb=" CB CYS A 190 " ideal model delta sinusoidal sigma weight residual 93.00 123.38 -30.38 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 567 0.032 - 0.063: 210 0.063 - 0.095: 58 0.095 - 0.127: 50 0.127 - 0.159: 5 Chirality restraints: 890 Sorted by residual: chirality pdb=" CB ILE A 97 " pdb=" CA ILE A 97 " pdb=" CG1 ILE A 97 " pdb=" CG2 ILE A 97 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA VAL A 462 " pdb=" N VAL A 462 " pdb=" C VAL A 462 " pdb=" CB VAL A 462 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 887 not shown) Planarity restraints: 1073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 511 " 0.049 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO A 512 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 439 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.60e+00 pdb=" N PRO A 440 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 590 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 591 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.030 5.00e-02 4.00e+02 ... (remaining 1070 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 195 2.71 - 3.26: 5396 3.26 - 3.81: 9341 3.81 - 4.35: 11932 4.35 - 4.90: 20828 Nonbonded interactions: 47692 Sorted by model distance: nonbonded pdb=" OE2 GLU A 476 " pdb=" OG SER A 539 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR A 477 " pdb=" O ALA A 662 " model vdw 2.184 3.040 nonbonded pdb=" O TYR A 548 " pdb=" OH TYR A 615 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR A 340 " pdb=" O SER B 104 " model vdw 2.243 3.040 nonbonded pdb=" O SER B 52 " pdb=" NH2 ARG B 72 " model vdw 2.271 3.120 ... (remaining 47687 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: 2.290 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.810 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.003 0.084 6035 Z= 0.113 Angle : 0.533 11.361 8233 Z= 0.276 Chirality : 0.043 0.159 890 Planarity : 0.005 0.072 1073 Dihedral : 12.738 76.633 2184 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.18 (0.30), residues: 749 helix: -2.79 (0.99), residues: 13 sheet: 0.34 (0.30), residues: 311 loop : -0.32 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.010 0.001 TYR B 116 PHE 0.011 0.001 PHE A 206 TRP 0.011 0.001 TRP A 300 HIS 0.003 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 6023) covalent geometry : angle 0.53220 / 0.28 ( 8209) SS BOND : bond 0.00170 / 0.09 ( 12) SS BOND : angle 0.73147 / 0.42 ( 24) hydrogen bonds : bond 0.23743 / 15.59 ( 197) hydrogen bonds : angle 9.53799 / 6.73 ( 543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.148 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.5770 time to fit residues: 46.4129 Evaluate side-chains 61 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 533 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134772 restraints weight = 6199.496| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.87 r_work: 0.3381 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6035 Z= 0.166 Angle : 0.585 10.178 8233 Z= 0.305 Chirality : 0.046 0.154 890 Planarity : 0.005 0.047 1073 Dihedral : 4.445 18.471 826 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.10 % Allowed : 9.23 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.31 (0.30), residues: 749 helix: -2.47 (1.06), residues: 15 sheet: 0.28 (0.30), residues: 303 loop : -0.43 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 332 TYR 0.013 0.002 TYR B 106 PHE 0.011 0.002 PHE B 29 TRP 0.007 0.001 TRP A 515 HIS 0.006 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6023) covalent geometry : angle 0.58501 / 0.30 ( 8209) SS BOND : bond 0.00221 / 0.10 ( 12) SS BOND : angle 0.69413 / 0.42 ( 24) hydrogen bonds : bond 0.04141 / 2.70 ( 197) hydrogen bonds : angle 6.57349 / 4.71 ( 543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.223 Fit side-chains REVERT: A 346 ASN cc_start: 0.6878 (t0) cc_final: 0.6570 (t0) REVERT: B 111 TYR cc_start: 0.8045 (p90) cc_final: 0.7814 (p90) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.4611 time to fit residues: 35.2204 Evaluate side-chains 63 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.175750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135331 restraints weight = 6185.444| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.90 r_work: 0.3401 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 0.035 6035 Z= 0.161 Angle : 0.564 9.286 8233 Z= 0.293 Chirality : 0.045 0.149 890 Planarity : 0.004 0.043 1073 Dihedral : 4.415 18.623 826 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 11.11 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.49 (0.30), residues: 749 helix: -2.41 (1.12), residues: 15 sheet: 0.10 (0.29), residues: 307 loop : -0.50 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.012 0.001 TYR A 615 PHE 0.009 0.002 PHE B 37 TRP 0.008 0.001 TRP A 515 HIS 0.006 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6023) covalent geometry : angle 0.56357 / 0.29 ( 8209) SS BOND : bond 0.00215 / 0.10 ( 12) SS BOND : angle 0.60501 / 0.36 ( 24) hydrogen bonds : bond 0.03755 / 2.49 ( 197) hydrogen bonds : angle 6.16653 / 4.44 ( 543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.238 Fit side-chains REVERT: A 346 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6578 (t0) REVERT: A 453 MET cc_start: 0.5718 (ppp) cc_final: 0.4381 (ttm) REVERT: B 111 TYR cc_start: 0.8071 (p90) cc_final: 0.7789 (p90) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.4547 time to fit residues: 34.2230 Evaluate side-chains 68 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.176348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135175 restraints weight = 6186.581| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.67 r_work: 0.3396 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6035 Z= 0.141 Angle : 0.543 8.718 8233 Z= 0.281 Chirality : 0.044 0.144 890 Planarity : 0.004 0.040 1073 Dihedral : 4.317 18.394 826 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 12.83 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.54 (0.29), residues: 749 helix: -2.34 (1.12), residues: 15 sheet: -0.03 (0.29), residues: 308 loop : -0.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.016 0.001 TYR A 615 PHE 0.008 0.001 PHE B 37 TRP 0.007 0.001 TRP A 515 HIS 0.005 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6023) covalent geometry : angle 0.54302 / 0.28 ( 8209) SS BOND : bond 0.00181 / 0.08 ( 12) SS BOND : angle 0.56295 / 0.35 ( 24) hydrogen bonds : bond 0.03354 / 2.22 ( 197) hydrogen bonds : angle 5.84198 / 4.23 ( 543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.298 Fit side-chains REVERT: A 346 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6289 (t0) REVERT: A 453 MET cc_start: 0.5694 (ppp) cc_final: 0.4468 (ttm) REVERT: B 111 TYR cc_start: 0.7955 (p90) cc_final: 0.7705 (p90) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 0.4035 time to fit residues: 32.7695 Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134284 restraints weight = 6288.083| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.69 r_work: 0.3428 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6035 Z= 0.155 Angle : 0.565 13.546 8233 Z= 0.287 Chirality : 0.045 0.145 890 Planarity : 0.004 0.039 1073 Dihedral : 4.366 18.785 826 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.97 % Allowed : 12.83 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.59 (0.29), residues: 749 helix: -2.40 (1.10), residues: 15 sheet: -0.09 (0.29), residues: 308 loop : -0.47 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.012 0.001 TYR A 548 PHE 0.008 0.002 PHE B 37 TRP 0.007 0.001 TRP A 515 HIS 0.005 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 6023) covalent geometry : angle 0.56464 / 0.29 ( 8209) SS BOND : bond 0.00210 / 0.10 ( 12) SS BOND : angle 0.60188 / 0.38 ( 24) hydrogen bonds : bond 0.03291 / 2.16 ( 197) hydrogen bonds : angle 5.74090 / 4.17 ( 543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.254 Fit side-chains REVERT: A 453 MET cc_start: 0.5560 (ppp) cc_final: 0.4475 (ttm) REVERT: B 111 TYR cc_start: 0.8000 (p90) cc_final: 0.7747 (p90) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.4548 time to fit residues: 36.1909 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.176889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136069 restraints weight = 6194.761| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.75 r_work: 0.3412 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6035 Z= 0.132 Angle : 0.540 11.861 8233 Z= 0.276 Chirality : 0.044 0.144 890 Planarity : 0.004 0.038 1073 Dihedral : 4.251 17.767 826 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.82 % Allowed : 13.62 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.55 (0.29), residues: 749 helix: -2.41 (1.10), residues: 15 sheet: -0.05 (0.29), residues: 308 loop : -0.44 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.011 0.001 TYR A 362 PHE 0.008 0.001 PHE B 37 TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6023) covalent geometry : angle 0.54014 / 0.28 ( 8209) SS BOND : bond 0.00184 / 0.09 ( 12) SS BOND : angle 0.55478 / 0.35 ( 24) hydrogen bonds : bond 0.03136 / 2.06 ( 197) hydrogen bonds : angle 5.55775 / 4.04 ( 543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.225 Fit side-chains REVERT: A 453 MET cc_start: 0.5511 (ppp) cc_final: 0.4505 (ttm) REVERT: B 111 TYR cc_start: 0.8048 (p90) cc_final: 0.7782 (p90) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.4389 time to fit residues: 36.9122 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133649 restraints weight = 6235.844| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.78 r_work: 0.3522 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6035 Z= 0.132 Angle : 0.569 11.442 8233 Z= 0.290 Chirality : 0.044 0.162 890 Planarity : 0.004 0.037 1073 Dihedral : 4.408 27.447 826 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.13 % Allowed : 14.40 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.52 (0.29), residues: 749 helix: -2.47 (1.08), residues: 15 sheet: -0.01 (0.29), residues: 299 loop : -0.43 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 363 TYR 0.011 0.001 TYR A 362 PHE 0.008 0.001 PHE B 37 TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6023) covalent geometry : angle 0.56492 / 0.29 ( 8209) SS BOND : bond 0.00273 / 0.13 ( 12) SS BOND : angle 1.41954 / 0.80 ( 24) hydrogen bonds : bond 0.03207 / 2.04 ( 197) hydrogen bonds : angle 5.68492 / 4.09 ( 543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.241 Fit side-chains REVERT: A 453 MET cc_start: 0.5306 (ppp) cc_final: 0.4566 (ttm) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.4474 time to fit residues: 37.5554 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 56 optimal weight: 0.0050 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN A 346 ASN A 356 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.179647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140467 restraints weight = 6121.731| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.68 r_work: 0.3441 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6035 Z= 0.111 Angle : 0.563 11.183 8233 Z= 0.280 Chirality : 0.044 0.141 890 Planarity : 0.004 0.036 1073 Dihedral : 4.277 24.109 826 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.35 % Allowed : 15.96 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.29), residues: 749 helix: -2.49 (1.08), residues: 15 sheet: -0.04 (0.29), residues: 302 loop : -0.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.010 0.001 TYR A 362 PHE 0.007 0.001 PHE B 37 TRP 0.005 0.001 TRP B 36 HIS 0.003 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6023) covalent geometry : angle 0.55997 / 0.28 ( 8209) SS BOND : bond 0.00214 / 0.11 ( 12) SS BOND : angle 1.27742 / 0.75 ( 24) hydrogen bonds : bond 0.03003 / 1.95 ( 197) hydrogen bonds : angle 5.60207 / 4.03 ( 543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.172 Fit side-chains REVERT: A 236 MET cc_start: 0.8344 (tpt) cc_final: 0.7825 (tpt) REVERT: A 346 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6557 (t0) REVERT: A 453 MET cc_start: 0.5189 (ppp) cc_final: 0.4660 (ttm) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.4246 time to fit residues: 32.5458 Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.177240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137510 restraints weight = 6269.389| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.67 r_work: 0.3425 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6035 Z= 0.138 Angle : 0.578 10.976 8233 Z= 0.287 Chirality : 0.044 0.143 890 Planarity : 0.004 0.037 1073 Dihedral : 4.328 21.323 826 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.35 % Allowed : 16.43 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.55 (0.30), residues: 749 helix: -2.48 (1.09), residues: 15 sheet: -0.05 (0.29), residues: 302 loop : -0.45 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.012 0.001 TYR A 362 PHE 0.007 0.001 PHE B 37 TRP 0.005 0.001 TRP A 515 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6023) covalent geometry : angle 0.57506 / 0.29 ( 8209) SS BOND : bond 0.00237 / 0.11 ( 12) SS BOND : angle 1.20196 / 0.72 ( 24) hydrogen bonds : bond 0.03041 / 1.96 ( 197) hydrogen bonds : angle 5.64721 / 4.07 ( 543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.149 Fit side-chains REVERT: A 453 MET cc_start: 0.5213 (ppp) cc_final: 0.4655 (ttm) outliers start: 15 outliers final: 14 residues processed: 69 average time/residue: 0.4081 time to fit residues: 29.9827 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.178749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139192 restraints weight = 6242.755| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.66 r_work: 0.3438 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6035 Z= 0.126 Angle : 0.559 10.804 8233 Z= 0.280 Chirality : 0.044 0.151 890 Planarity : 0.004 0.036 1073 Dihedral : 4.245 19.343 826 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 16.43 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.30), residues: 749 helix: -2.49 (1.09), residues: 15 sheet: -0.04 (0.29), residues: 302 loop : -0.43 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.013 0.001 TYR A 362 PHE 0.007 0.001 PHE B 37 TRP 0.005 0.001 TRP A 515 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6023) covalent geometry : angle 0.55625 / 0.28 ( 8209) SS BOND : bond 0.00216 / 0.11 ( 12) SS BOND : angle 1.13741 / 0.68 ( 24) hydrogen bonds : bond 0.02960 / 1.91 ( 197) hydrogen bonds : angle 5.60204 / 4.03 ( 543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.228 Fit side-chains REVERT: A 236 MET cc_start: 0.8358 (tpt) cc_final: 0.7881 (tpt) REVERT: A 346 ASN cc_start: 0.6722 (t0) cc_final: 0.6489 (t0) REVERT: A 453 MET cc_start: 0.5129 (ppp) cc_final: 0.4663 (ttm) REVERT: B 112 ASP cc_start: 0.8156 (t0) cc_final: 0.7789 (t70) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.4113 time to fit residues: 32.0091 Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.179296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139181 restraints weight = 6181.781| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.57 r_work: 0.3553 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6035 Z= 0.119 Angle : 0.551 10.825 8233 Z= 0.276 Chirality : 0.044 0.141 890 Planarity : 0.004 0.036 1073 Dihedral : 4.184 17.364 826 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 16.59 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.46 (0.30), residues: 749 helix: -2.55 (1.07), residues: 15 sheet: 0.03 (0.29), residues: 311 loop : -0.40 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.012 0.001 TYR A 362 PHE 0.007 0.001 PHE B 37 TRP 0.005 0.001 TRP A 515 HIS 0.003 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6023) covalent geometry : angle 0.54865 / 0.27 ( 8209) SS BOND : bond 0.00191 / 0.10 ( 12) SS BOND : angle 1.09589 / 0.65 ( 24) hydrogen bonds : bond 0.02885 / 1.87 ( 197) hydrogen bonds : angle 5.54924 / 3.99 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.86 seconds wall clock time: 35 minutes 47.22 seconds (2147.22 seconds total)