Starting phenix.real_space_refine on Tue Mar 3 14:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.map" model { file = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2026/7dxi_30910.cif" } resolution = 3.53 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= 0.002 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 24 5.16 5 C 3920 2.51 5 N 1064 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3064 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.15, per 1000 atoms: 0.35 Number of scatterers: 6130 At special positions: 0 Unit cell: (115.333, 115.333, 59.9472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 24 16.00 O 1120 8.00 N 1064 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 515 " 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: 0.48 Conformation dependent library (CDL) restraints added in 371.6 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 45.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.715A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 166' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.750A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.615A pdb=" N MET A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.716A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 165 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 166' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.749A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 428 through 435 Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.616A pdb=" N MET B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA A 66 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL A 120 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR A 68 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 117 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 139 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 119 " --> pdb=" O VAL A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA B 66 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 120 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 68 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 117 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 139 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 119 " --> pdb=" O VAL B 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA7, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 168 hydrogen bonds defined for protein. 480 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: 0.83 Time building geometry restraints manager: 0.66 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: 1962 1.34 - 1.46: 1218 1.46 - 1.58: 3066 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6286 Sorted by residual: bond pdb=" C GLN B 458 " pdb=" N PRO B 459 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.18e-02 7.18e+03 3.35e+00 bond pdb=" C GLN A 458 " pdb=" N PRO A 459 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.18e-02 7.18e+03 3.26e+00 bond pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.55e+00 bond pdb=" CA LYS B 368 " pdb=" C LYS B 368 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.52e+00 bond pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.31e-02 5.83e+03 2.34e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 8384 4.00 - 8.01: 125 8.01 - 12.01: 19 12.01 - 16.01: 6 16.01 - 20.01: 2 Bond angle restraints: 8536 Sorted by residual: angle pdb=" C PRO A 459 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" C PRO B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 112.00 105.33 6.67 1.40e+00 5.10e-01 2.27e+01 angle pdb=" CA PRO B 460 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" N LYS A 368 " pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 110.80 120.35 -9.55 2.13e+00 2.20e-01 2.01e+01 ... (remaining 8531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3329 17.70 - 35.40: 365 35.40 - 53.11: 64 53.11 - 70.81: 12 70.81 - 88.51: 4 Dihedral angle restraints: 3774 sinusoidal: 1554 harmonic: 2220 Sorted by residual: dihedral pdb=" CA PHE A 367 " pdb=" C PHE A 367 " pdb=" N LYS A 368 " pdb=" CA LYS A 368 " ideal model delta harmonic sigma weight residual -180.00 -128.71 -51.29 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N LYS B 368 " pdb=" CA LYS B 368 " ideal model delta harmonic sigma weight residual -180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 515 " pdb=" CB CYS A 515 " ideal model delta sinusoidal sigma weight residual 93.00 -178.49 -88.51 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 629 0.053 - 0.105: 217 0.105 - 0.158: 63 0.158 - 0.211: 13 0.211 - 0.263: 10 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" C LYS A 368 " pdb=" CB LYS A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 368 " pdb=" N LYS B 368 " pdb=" C LYS B 368 " pdb=" CB LYS B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN B 458 " pdb=" N GLN B 458 " pdb=" C GLN B 458 " pdb=" CB GLN B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 929 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 459 " -0.130 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO A 460 " 0.342 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 459 " 0.130 5.00e-02 4.00e+02 1.98e-01 6.25e+01 pdb=" N PRO B 460 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 151 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 152 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.065 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 2 2.15 - 2.84: 1965 2.84 - 3.53: 7955 3.53 - 4.21: 13695 4.21 - 4.90: 23490 Nonbonded interactions: 47107 Sorted by model distance: nonbonded pdb=" OD2 ASP B 439 " pdb=" OG1 THR B 443 " model vdw 1.468 3.040 nonbonded pdb=" OD2 ASP A 439 " pdb=" OG1 THR A 443 " model vdw 1.468 3.040 nonbonded pdb=" CB ASP A 439 " pdb="CA CA A 701 " model vdw 2.247 2.910 nonbonded pdb=" O THR B 443 " pdb="CA CA B 701 " model vdw 2.248 2.510 nonbonded pdb=" CB ASP B 439 " pdb="CA CA B 701 " model vdw 2.248 2.910 ... (remaining 47102 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.006 0.040 6288 Z= 0.288 Angle : 1.299 20.014 8540 Z= 0.676 Chirality : 0.064 0.263 932 Planarity : 0.012 0.198 1106 Dihedral : 15.064 76.380 2316 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.91 % Favored : 85.54 % Rotamer: Outliers : 0.30 % Allowed : 0.74 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 1.44 % 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: -5.04 (0.24), residues: 726 helix: -3.36 (0.19), residues: 304 sheet: -2.64 (0.75), residues: 36 loop : -3.47 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 467 TYR 0.064 0.004 TYR A 175 PHE 0.052 0.004 PHE B 436 TRP 0.037 0.004 TRP A 463 HIS 0.014 0.002 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 6286) covalent geometry : angle 1.29834 ( 8536) SS BOND : bond 0.00269 ( 2) SS BOND : angle 2.47628 ( 4) hydrogen bonds : bond 0.18249 ( 168) hydrogen bonds : angle 7.73206 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6946 (t0) REVERT: A 368 LYS cc_start: 0.6373 (pttp) cc_final: 0.6167 (pttp) REVERT: A 594 ASP cc_start: 0.8115 (t70) cc_final: 0.7628 (m-30) REVERT: B 149 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7037 (t0) REVERT: B 463 TRP cc_start: 0.6358 (p-90) cc_final: 0.6064 (p-90) REVERT: B 589 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7754 (mtp180) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.0801 time to fit residues: 12.5016 Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain B residue 149 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 576 ASN B 116 HIS B 576 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115506 restraints weight = 9130.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118445 restraints weight = 5821.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120391 restraints weight = 4370.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121665 restraints weight = 3624.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122451 restraints weight = 3199.133| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6288 Z= 0.149 Angle : 0.772 12.267 8540 Z= 0.383 Chirality : 0.045 0.159 932 Planarity : 0.009 0.154 1106 Dihedral : 7.904 47.272 834 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.64 % Favored : 85.81 % Rotamer: Outliers : 1.79 % Allowed : 8.04 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % 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: -3.95 (0.28), residues: 726 helix: -2.15 (0.24), residues: 324 sheet: -2.43 (0.86), residues: 32 loop : -3.14 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.024 0.002 TYR B 412 PHE 0.017 0.002 PHE A 595 TRP 0.016 0.002 TRP A 70 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6286) covalent geometry : angle 0.77169 ( 8536) SS BOND : bond 0.00007 ( 2) SS BOND : angle 1.00822 ( 4) hydrogen bonds : bond 0.03206 ( 168) hydrogen bonds : angle 4.71165 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: A 576 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 594 ASP cc_start: 0.8218 (t70) cc_final: 0.7926 (t0) REVERT: B 576 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 594 ASP cc_start: 0.8276 (t70) cc_final: 0.8047 (t0) outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.0715 time to fit residues: 11.5693 Evaluate side-chains 99 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 576 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.0770 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 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 = 0.3731 r_free = 0.3731 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121386 restraints weight = 8924.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124426 restraints weight = 5687.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126449 restraints weight = 4235.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127724 restraints weight = 3481.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128652 restraints weight = 3060.538| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6288 Z= 0.126 Angle : 0.689 8.676 8540 Z= 0.353 Chirality : 0.044 0.183 932 Planarity : 0.006 0.099 1106 Dihedral : 7.402 49.409 834 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 1.49 % Allowed : 13.24 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % 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: -3.37 (0.29), residues: 726 helix: -1.46 (0.27), residues: 322 sheet: -3.04 (0.68), residues: 46 loop : -2.91 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 562 TYR 0.016 0.001 TYR A 412 PHE 0.015 0.001 PHE A 595 TRP 0.011 0.001 TRP A 70 HIS 0.002 0.000 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6286) covalent geometry : angle 0.68928 ( 8536) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.40665 ( 4) hydrogen bonds : bond 0.02577 ( 168) hydrogen bonds : angle 4.24081 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: B 423 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 471 GLU cc_start: 0.6026 (tm-30) cc_final: 0.5778 (tm-30) REVERT: B 514 ARG cc_start: 0.5421 (ttt180) cc_final: 0.5156 (ptp-110) REVERT: B 576 ASN cc_start: 0.8463 (t0) cc_final: 0.8167 (t0) REVERT: B 594 ASP cc_start: 0.8212 (t70) cc_final: 0.7911 (t0) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.0647 time to fit residues: 10.7538 Evaluate side-chains 100 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 526 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 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 = 0.3676 r_free = 0.3676 target = 0.141034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116435 restraints weight = 9010.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119369 restraints weight = 5778.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121314 restraints weight = 4351.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122598 restraints weight = 3613.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123339 restraints weight = 3191.690| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6288 Z= 0.145 Angle : 0.710 8.078 8540 Z= 0.363 Chirality : 0.045 0.158 932 Planarity : 0.006 0.102 1106 Dihedral : 7.391 55.692 834 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 2.38 % Allowed : 14.58 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.11 (0.30), residues: 726 helix: -1.11 (0.27), residues: 328 sheet: -2.85 (0.71), residues: 42 loop : -2.95 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.022 0.002 TYR B 412 PHE 0.013 0.001 PHE B 600 TRP 0.012 0.001 TRP B 444 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6286) covalent geometry : angle 0.70990 ( 8536) SS BOND : bond 0.00015 ( 2) SS BOND : angle 0.53800 ( 4) hydrogen bonds : bond 0.02772 ( 168) hydrogen bonds : angle 4.23476 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 554 THR cc_start: 0.7354 (m) cc_final: 0.6622 (m) REVERT: A 558 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: A 576 ASN cc_start: 0.8572 (t0) cc_final: 0.8326 (t0) REVERT: B 471 GLU cc_start: 0.6083 (tm-30) cc_final: 0.5851 (tm-30) REVERT: B 576 ASN cc_start: 0.8563 (t0) cc_final: 0.8319 (t0) REVERT: B 594 ASP cc_start: 0.8174 (t70) cc_final: 0.7912 (t0) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.0585 time to fit residues: 9.1854 Evaluate side-chains 103 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119621 restraints weight = 9262.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122699 restraints weight = 5888.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124814 restraints weight = 4389.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126111 restraints weight = 3604.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126699 restraints weight = 3167.275| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6288 Z= 0.121 Angle : 0.660 7.960 8540 Z= 0.340 Chirality : 0.043 0.163 932 Planarity : 0.006 0.097 1106 Dihedral : 7.072 57.795 834 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 2.53 % Allowed : 16.22 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.78 (0.30), residues: 726 helix: -0.77 (0.28), residues: 326 sheet: -2.99 (0.68), residues: 46 loop : -2.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.017 0.001 TYR B 412 PHE 0.011 0.001 PHE B 419 TRP 0.009 0.001 TRP A 70 HIS 0.002 0.001 HIS B 590 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6286) covalent geometry : angle 0.66021 ( 8536) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.22558 ( 4) hydrogen bonds : bond 0.02477 ( 168) hydrogen bonds : angle 4.08858 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: B 118 TYR cc_start: 0.8730 (m-80) cc_final: 0.8397 (m-80) REVERT: B 467 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7524 (tpp80) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 0.0611 time to fit residues: 10.6478 Evaluate side-chains 109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113215 restraints weight = 9155.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116126 restraints weight = 5869.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118009 restraints weight = 4420.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119316 restraints weight = 3681.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120096 restraints weight = 3245.530| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6288 Z= 0.183 Angle : 0.737 8.321 8540 Z= 0.381 Chirality : 0.046 0.149 932 Planarity : 0.007 0.106 1106 Dihedral : 7.277 50.776 834 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.84 % Favored : 84.16 % Rotamer: Outliers : 3.72 % Allowed : 16.07 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.82 (0.30), residues: 726 helix: -0.73 (0.28), residues: 326 sheet: -2.92 (0.70), residues: 42 loop : -2.90 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 562 TYR 0.024 0.002 TYR A 412 PHE 0.016 0.002 PHE A 600 TRP 0.015 0.001 TRP A 444 HIS 0.003 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6286) covalent geometry : angle 0.73621 ( 8536) SS BOND : bond 0.00844 ( 2) SS BOND : angle 1.82844 ( 4) hydrogen bonds : bond 0.03022 ( 168) hydrogen bonds : angle 4.26984 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: B 118 TYR cc_start: 0.8795 (m-80) cc_final: 0.8480 (m-80) REVERT: B 467 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7554 (tpp80) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 0.0603 time to fit residues: 10.0347 Evaluate side-chains 109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114264 restraints weight = 9161.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117152 restraints weight = 5899.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119169 restraints weight = 4453.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120456 restraints weight = 3682.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121211 restraints weight = 3245.608| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6288 Z= 0.163 Angle : 0.721 9.138 8540 Z= 0.373 Chirality : 0.045 0.154 932 Planarity : 0.007 0.109 1106 Dihedral : 6.987 39.988 834 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Rotamer: Outliers : 2.83 % Allowed : 18.15 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.74 (0.30), residues: 726 helix: -0.62 (0.28), residues: 324 sheet: -3.06 (0.70), residues: 42 loop : -2.87 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.021 0.002 TYR A 412 PHE 0.013 0.001 PHE B 419 TRP 0.012 0.002 TRP A 444 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6286) covalent geometry : angle 0.72119 ( 8536) SS BOND : bond 0.00602 ( 2) SS BOND : angle 0.95654 ( 4) hydrogen bonds : bond 0.02846 ( 168) hydrogen bonds : angle 4.26624 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: B 118 TYR cc_start: 0.8795 (m-80) cc_final: 0.8469 (m-80) REVERT: B 423 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7396 (tp30) REVERT: B 467 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7619 (tpp80) REVERT: B 511 LEU cc_start: 0.8044 (tt) cc_final: 0.7539 (tt) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.0549 time to fit residues: 9.3094 Evaluate side-chains 110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 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 = 0.3676 r_free = 0.3676 target = 0.141499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116952 restraints weight = 9106.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120013 restraints weight = 5729.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121961 restraints weight = 4254.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123370 restraints weight = 3525.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123704 restraints weight = 3087.550| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6288 Z= 0.142 Angle : 0.735 10.910 8540 Z= 0.376 Chirality : 0.045 0.155 932 Planarity : 0.007 0.114 1106 Dihedral : 6.440 34.343 830 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 1.93 % Allowed : 19.35 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.74 (0.30), residues: 726 helix: -0.66 (0.28), residues: 334 sheet: -3.02 (0.70), residues: 42 loop : -2.90 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.018 0.001 TYR A 412 PHE 0.011 0.001 PHE B 419 TRP 0.010 0.001 TRP A 70 HIS 0.002 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6286) covalent geometry : angle 0.73381 ( 8536) SS BOND : bond 0.00561 ( 2) SS BOND : angle 1.69873 ( 4) hydrogen bonds : bond 0.02768 ( 168) hydrogen bonds : angle 4.18838 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: B 118 TYR cc_start: 0.8752 (m-80) cc_final: 0.8433 (m-80) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.0550 time to fit residues: 8.9414 Evaluate side-chains 107 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 0.0020 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122660 restraints weight = 9006.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125887 restraints weight = 5658.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128011 restraints weight = 4182.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129392 restraints weight = 3424.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130215 restraints weight = 2998.262| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6288 Z= 0.131 Angle : 0.709 10.877 8540 Z= 0.366 Chirality : 0.044 0.165 932 Planarity : 0.007 0.114 1106 Dihedral : 6.039 30.049 830 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 2.38 % Allowed : 19.20 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.51 (0.31), residues: 726 helix: -0.42 (0.28), residues: 328 sheet: -3.16 (0.66), residues: 46 loop : -2.74 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.015 0.001 TYR B 412 PHE 0.009 0.001 PHE A 595 TRP 0.014 0.001 TRP B 463 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6286) covalent geometry : angle 0.70908 ( 8536) SS BOND : bond 0.00488 ( 2) SS BOND : angle 1.25140 ( 4) hydrogen bonds : bond 0.02620 ( 168) hydrogen bonds : angle 4.08588 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: B 118 TYR cc_start: 0.8720 (m-80) cc_final: 0.8409 (m-80) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.0529 time to fit residues: 10.2057 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 576 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122125 restraints weight = 9023.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125303 restraints weight = 5712.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127386 restraints weight = 4246.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128718 restraints weight = 3494.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129635 restraints weight = 3079.276| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6288 Z= 0.135 Angle : 0.748 11.871 8540 Z= 0.375 Chirality : 0.045 0.153 932 Planarity : 0.006 0.093 1106 Dihedral : 5.916 29.718 830 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % Rotamer: Outliers : 1.93 % Allowed : 20.09 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.31), residues: 726 helix: -0.33 (0.29), residues: 326 sheet: -2.98 (0.69), residues: 46 loop : -2.79 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.016 0.001 TYR A 412 PHE 0.009 0.001 PHE A 419 TRP 0.031 0.002 TRP B 463 HIS 0.005 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6286) covalent geometry : angle 0.74829 ( 8536) SS BOND : bond 0.00484 ( 2) SS BOND : angle 0.97055 ( 4) hydrogen bonds : bond 0.02685 ( 168) hydrogen bonds : angle 4.12927 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: B 118 TYR cc_start: 0.8711 (m-80) cc_final: 0.8396 (m-80) REVERT: B 411 GLN cc_start: 0.6195 (mt0) cc_final: 0.5909 (mt0) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.0519 time to fit residues: 8.7840 Evaluate side-chains 112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 576 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN ** B 576 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114488 restraints weight = 9118.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117466 restraints weight = 5890.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119435 restraints weight = 4436.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120691 restraints weight = 3686.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121414 restraints weight = 3278.360| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6288 Z= 0.183 Angle : 0.794 11.560 8540 Z= 0.398 Chirality : 0.047 0.159 932 Planarity : 0.007 0.119 1106 Dihedral : 6.422 33.423 830 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.12 % Favored : 83.88 % Rotamer: Outliers : 1.79 % Allowed : 20.54 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.70 (0.30), residues: 726 helix: -0.57 (0.28), residues: 332 sheet: -3.18 (0.67), residues: 46 loop : -2.89 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.023 0.002 TYR A 412 PHE 0.014 0.002 PHE B 600 TRP 0.034 0.002 TRP B 463 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6286) covalent geometry : angle 0.79384 ( 8536) SS BOND : bond 0.00595 ( 2) SS BOND : angle 1.31155 ( 4) hydrogen bonds : bond 0.03123 ( 168) hydrogen bonds : angle 4.41003 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.17 seconds wall clock time: 19 minutes 40.17 seconds (1180.17 seconds total)