Starting phenix.real_space_refine on Thu Jul 2 03:10:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.map" model { file = "/net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yq5_73324/07_2026/9yq5_73324.cif" } resolution = 2.8 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= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 2 5.49 5 S 35 5.16 5 C 3894 2.51 5 N 991 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6034 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 bond proxies already assigned to first conformer: 4152 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'UGA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 341 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 341 " occ=0.50 Time building chain proxies: 2.08, per 1000 atoms: 0.34 Number of scatterers: 6034 At special positions: 0 Unit cell: (71.28, 93.96, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 35 16.00 P 2 15.00 O 1110 8.00 N 991 7.00 C 3894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.51 Conformation dependent library (CDL) restraints added in 544.9 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 48.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.764A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.656A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.572A pdb=" N SER A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.710A pdb=" N TRP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.547A pdb=" N GLU A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 331 through 356 removed outlier: 4.652A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.518A pdb=" N HIS A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 361 " --> pdb=" O TRP A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 361' Processing helix chain 'A' and resid 364 through 391 removed outlier: 3.969A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.640A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 removed outlier: 3.816A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.590A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.681A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 4.019A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 7.787A pdb=" N VAL A 84 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 116 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 86 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N CYS A 118 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 88 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE A 120 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 90 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.201A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.801A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.937A pdb=" N VAL B 12 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR B 121 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TRP B 114 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA B 97 " --> pdb=" O TRP B 114 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLN B 116 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 95 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 52 removed outlier: 6.620A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 892 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: 0.94 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1865 1.34 - 1.46: 1655 1.46 - 1.58: 2613 1.58 - 1.70: 1 1.70 - 1.81: 55 Bond restraints: 6189 Sorted by residual: bond pdb=" O5D UGA A 601 " pdb=" PA UGA A 601 " ideal model delta sigma weight residual 1.645 1.749 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CAI Y01 A 602 " pdb=" CAK Y01 A 602 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O3A UGA A 601 " pdb=" PA UGA A 601 " ideal model delta sigma weight residual 1.652 1.569 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3B UGA A 601 " pdb=" PB UGA A 601 " ideal model delta sigma weight residual 1.646 1.713 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CAI Y01 A 602 " pdb=" CAZ Y01 A 602 " ideal model delta sigma weight residual 1.332 1.383 -0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 8394 4.70 - 9.40: 15 9.40 - 14.10: 4 14.10 - 18.80: 0 18.80 - 23.50: 1 Bond angle restraints: 8414 Sorted by residual: angle pdb=" PA UGA A 601 " pdb=" O3A UGA A 601 " pdb=" PB UGA A 601 " ideal model delta sigma weight residual 123.32 146.82 -23.50 3.00e+00 1.11e-01 6.14e+01 angle pdb=" OAG Y01 A 602 " pdb=" CAY Y01 A 602 " pdb=" OAW Y01 A 602 " ideal model delta sigma weight residual 123.38 111.47 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CAM Y01 A 602 " pdb=" CAY Y01 A 602 " pdb=" OAW Y01 A 602 " ideal model delta sigma weight residual 111.19 122.88 -11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O2A UGA A 601 " pdb=" PA UGA A 601 " pdb=" O5D UGA A 601 " ideal model delta sigma weight residual 109.54 98.27 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CAV Y01 A 602 " pdb=" CAZ Y01 A 602 " pdb=" CBH Y01 A 602 " ideal model delta sigma weight residual 116.96 126.60 -9.64 3.00e+00 1.11e-01 1.03e+01 ... (remaining 8409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3193 17.77 - 35.53: 349 35.53 - 53.29: 104 53.29 - 71.06: 22 71.06 - 88.82: 5 Dihedral angle restraints: 3673 sinusoidal: 1506 harmonic: 2167 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 53.13 39.87 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CA ASP C 59 " pdb=" CB ASP C 59 " pdb=" CG ASP C 59 " pdb=" OD1 ASP C 59 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PRO B 41 " pdb=" C PRO B 41 " pdb=" N GLY B 42 " pdb=" CA GLY B 42 " ideal model delta harmonic sigma weight residual 180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 853 0.082 - 0.164: 61 0.164 - 0.246: 2 0.246 - 0.328: 1 0.328 - 0.409: 2 Chirality restraints: 919 Sorted by residual: chirality pdb=" C2' UGA A 601 " pdb=" C1' UGA A 601 " pdb=" C3' UGA A 601 " pdb=" O2' UGA A 601 " both_signs ideal model delta sigma weight residual False -2.23 -2.64 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C1D UGA A 601 " pdb=" C2D UGA A 601 " pdb=" N1 UGA A 601 " pdb=" O4D UGA A 601 " both_signs ideal model delta sigma weight residual False 2.21 2.55 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C5' UGA A 601 " pdb=" C4' UGA A 601 " pdb=" C6' UGA A 601 " pdb=" O5' UGA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 916 not shown) Planarity restraints: 1038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 271 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 252 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C PHE A 252 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 252 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 253 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 434 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C TYR A 434 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR A 434 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 435 " -0.009 2.00e-02 2.50e+03 ... (remaining 1035 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 150 2.71 - 3.26: 5625 3.26 - 3.80: 9735 3.80 - 4.35: 12597 4.35 - 4.90: 21695 Nonbonded interactions: 49802 Sorted by model distance: nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 603 " model vdw 2.159 3.060 nonbonded pdb=" OE2 GLU A 207 " pdb=" NE1 TRP A 325 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.287 3.040 nonbonded pdb=" O LYS A 155 " pdb=" NE2 GLN A 186 " model vdw 2.303 3.120 nonbonded pdb=" OH TYR A 377 " pdb=" OAH Y01 A 602 " model vdw 2.324 3.040 ... (remaining 49797 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.030 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 6191 Z= 0.175 Angle : 0.647 23.499 8418 Z= 0.283 Chirality : 0.047 0.409 919 Planarity : 0.003 0.043 1038 Dihedral : 16.311 88.823 2289 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.79 % Allowed : 15.62 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.31), residues: 737 helix: 1.58 (0.29), residues: 325 sheet: 0.39 (0.43), residues: 148 loop : -0.64 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.012 0.001 TYR A 414 PHE 0.010 0.001 PHE A 49 TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 ( 6189) covalent geometry : angle 0.64727 / 0.28 ( 8414) SS BOND : bond 0.00111 / 0.06 ( 2) SS BOND : angle 0.22985 / 0.12 ( 4) hydrogen bonds : bond 0.12216 / 7.09 ( 323) hydrogen bonds : angle 5.06073 / 3.71 ( 892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.241 Fit side-chains REVERT: A 49 PHE cc_start: 0.7568 (t80) cc_final: 0.7245 (t80) outliers start: 5 outliers final: 5 residues processed: 70 average time/residue: 0.3306 time to fit residues: 25.1415 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.173525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129954 restraints weight = 11330.267| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.10 r_work: 0.3313 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6191 Z= 0.131 Angle : 0.488 10.134 8418 Z= 0.259 Chirality : 0.041 0.143 919 Planarity : 0.004 0.043 1038 Dihedral : 7.464 75.929 969 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 15.62 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.31), residues: 737 helix: 1.59 (0.29), residues: 326 sheet: 0.45 (0.42), residues: 148 loop : -0.72 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.015 0.001 TYR A 414 PHE 0.012 0.001 PHE A 49 TRP 0.012 0.001 TRP A 287 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6189) covalent geometry : angle 0.48855 / 0.26 ( 8414) SS BOND : bond 0.00167 / 0.09 ( 2) SS BOND : angle 0.27995 / 0.15 ( 4) hydrogen bonds : bond 0.04262 / 2.72 ( 323) hydrogen bonds : angle 4.38576 / 3.24 ( 892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.225 Fit side-chains REVERT: B 82 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7021 (mtp) outliers start: 6 outliers final: 1 residues processed: 71 average time/residue: 0.4008 time to fit residues: 30.5398 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.172797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120828 restraints weight = 13954.098| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.50 r_work: 0.3329 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6191 Z= 0.112 Angle : 0.467 11.689 8418 Z= 0.246 Chirality : 0.040 0.143 919 Planarity : 0.003 0.043 1038 Dihedral : 6.399 68.857 960 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.95 % Allowed : 15.46 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.31), residues: 737 helix: 1.63 (0.29), residues: 326 sheet: 0.43 (0.42), residues: 148 loop : -0.74 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.014 0.001 TYR A 414 PHE 0.011 0.001 PHE C 47 TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6189) covalent geometry : angle 0.46691 / 0.25 ( 8414) SS BOND : bond 0.00151 / 0.08 ( 2) SS BOND : angle 0.29946 / 0.17 ( 4) hydrogen bonds : bond 0.03902 / 2.49 ( 323) hydrogen bonds : angle 4.20014 / 3.09 ( 892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.178 Fit side-chains REVERT: A 49 PHE cc_start: 0.7828 (t80) cc_final: 0.7476 (t80) REVERT: A 129 LYS cc_start: 0.7568 (mtpt) cc_final: 0.7243 (mttm) REVERT: A 438 MET cc_start: 0.7980 (mmm) cc_final: 0.7570 (mmm) REVERT: B 82 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6771 (mtp) REVERT: C 113 TYR cc_start: 0.8514 (m-80) cc_final: 0.8298 (m-80) outliers start: 6 outliers final: 1 residues processed: 72 average time/residue: 0.4262 time to fit residues: 32.6153 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126571 restraints weight = 11782.753| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.47 r_work: 0.3267 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6191 Z= 0.148 Angle : 0.505 12.654 8418 Z= 0.265 Chirality : 0.041 0.142 919 Planarity : 0.004 0.043 1038 Dihedral : 6.465 69.531 959 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.58 % Allowed : 15.62 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.30), residues: 737 helix: 1.53 (0.29), residues: 326 sheet: 0.43 (0.42), residues: 148 loop : -0.78 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.015 0.001 TYR A 528 PHE 0.013 0.001 PHE A 49 TRP 0.012 0.001 TRP A 287 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6189) covalent geometry : angle 0.50500 / 0.26 ( 8414) SS BOND : bond 0.00220 / 0.12 ( 2) SS BOND : angle 0.43371 / 0.24 ( 4) hydrogen bonds : bond 0.04290 / 2.76 ( 323) hydrogen bonds : angle 4.29420 / 3.16 ( 892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.232 Fit side-chains REVERT: A 49 PHE cc_start: 0.7863 (t80) cc_final: 0.7514 (t80) REVERT: A 125 GLU cc_start: 0.7234 (tt0) cc_final: 0.6201 (mp0) REVERT: A 129 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7395 (mttm) REVERT: A 144 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7955 (ttmt) REVERT: B 82 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.7011 (mtp) outliers start: 10 outliers final: 3 residues processed: 75 average time/residue: 0.4043 time to fit residues: 32.3536 Evaluate side-chains 75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130754 restraints weight = 16485.585| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.27 r_work: 0.3285 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6191 Z= 0.123 Angle : 0.483 12.931 8418 Z= 0.253 Chirality : 0.040 0.140 919 Planarity : 0.003 0.042 1038 Dihedral : 6.326 69.345 959 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.79 % Allowed : 15.77 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.30), residues: 737 helix: 1.57 (0.29), residues: 326 sheet: 0.47 (0.42), residues: 148 loop : -0.79 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.015 0.001 TYR A 414 PHE 0.011 0.001 PHE A 49 TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 6189) covalent geometry : angle 0.48337 / 0.25 ( 8414) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.33064 / 0.19 ( 4) hydrogen bonds : bond 0.04005 / 2.57 ( 323) hydrogen bonds : angle 4.20801 / 3.09 ( 892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.268 Fit side-chains REVERT: A 49 PHE cc_start: 0.7763 (t80) cc_final: 0.7412 (t80) REVERT: A 125 GLU cc_start: 0.7209 (tt0) cc_final: 0.6144 (mp0) REVERT: A 129 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7298 (mttp) REVERT: A 438 MET cc_start: 0.7964 (mmm) cc_final: 0.7542 (mmm) REVERT: C 113 TYR cc_start: 0.8565 (m-80) cc_final: 0.8294 (m-80) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.4317 time to fit residues: 32.7517 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127550 restraints weight = 13612.628| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.55 r_work: 0.3286 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6191 Z= 0.140 Angle : 0.501 13.344 8418 Z= 0.262 Chirality : 0.041 0.141 919 Planarity : 0.004 0.043 1038 Dihedral : 6.344 69.460 959 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.10 % Allowed : 15.93 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 737 helix: 1.51 (0.29), residues: 326 sheet: 0.46 (0.42), residues: 148 loop : -0.79 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.015 0.001 TYR A 528 PHE 0.012 0.001 PHE A 49 TRP 0.012 0.001 TRP A 287 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6189) covalent geometry : angle 0.50151 / 0.26 ( 8414) SS BOND : bond 0.00222 / 0.12 ( 2) SS BOND : angle 0.41683 / 0.23 ( 4) hydrogen bonds : bond 0.04185 / 2.70 ( 323) hydrogen bonds : angle 4.24385 / 3.12 ( 892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.200 Fit side-chains REVERT: A 49 PHE cc_start: 0.7821 (t80) cc_final: 0.7479 (t80) REVERT: A 125 GLU cc_start: 0.7229 (tt0) cc_final: 0.6184 (mp0) REVERT: A 129 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7369 (mttp) REVERT: A 438 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7599 (mmm) REVERT: C 113 TYR cc_start: 0.8668 (m-80) cc_final: 0.8403 (m-80) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.4244 time to fit residues: 31.5696 Evaluate side-chains 72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128213 restraints weight = 13612.742| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.69 r_work: 0.3277 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6191 Z= 0.120 Angle : 0.481 13.356 8418 Z= 0.251 Chirality : 0.040 0.138 919 Planarity : 0.003 0.042 1038 Dihedral : 6.219 69.335 959 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.95 % Allowed : 15.93 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 737 helix: 1.57 (0.29), residues: 326 sheet: 0.49 (0.42), residues: 148 loop : -0.76 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.015 0.001 TYR A 414 PHE 0.011 0.001 PHE A 49 TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6189) covalent geometry : angle 0.48107 / 0.25 ( 8414) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 0.35800 / 0.20 ( 4) hydrogen bonds : bond 0.03953 / 2.54 ( 323) hydrogen bonds : angle 4.16627 / 3.06 ( 892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.216 Fit side-chains REVERT: A 49 PHE cc_start: 0.7828 (t80) cc_final: 0.7493 (t80) REVERT: A 129 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7272 (mttp) REVERT: A 438 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: C 113 TYR cc_start: 0.8703 (m-80) cc_final: 0.8441 (m-80) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.4101 time to fit residues: 31.0925 Evaluate side-chains 72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 11 optimal weight: 0.0770 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.172330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128557 restraints weight = 16358.074| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.19 r_work: 0.3290 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6191 Z= 0.137 Angle : 0.501 14.009 8418 Z= 0.260 Chirality : 0.041 0.141 919 Planarity : 0.003 0.043 1038 Dihedral : 6.261 69.561 959 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.26 % Allowed : 16.09 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.30), residues: 737 helix: 1.51 (0.29), residues: 326 sheet: 0.51 (0.42), residues: 148 loop : -0.77 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.015 0.001 TYR A 528 PHE 0.012 0.001 PHE A 49 TRP 0.011 0.001 TRP A 287 HIS 0.005 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6189) covalent geometry : angle 0.50147 / 0.26 ( 8414) SS BOND : bond 0.00218 / 0.11 ( 2) SS BOND : angle 0.41434 / 0.23 ( 4) hydrogen bonds : bond 0.04146 / 2.67 ( 323) hydrogen bonds : angle 4.21842 / 3.10 ( 892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.216 Fit side-chains REVERT: A 49 PHE cc_start: 0.7736 (t80) cc_final: 0.7400 (t80) REVERT: A 125 GLU cc_start: 0.7218 (tt0) cc_final: 0.6159 (mp0) REVERT: A 129 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7222 (mttm) REVERT: A 144 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7914 (ttmt) REVERT: A 438 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7579 (mmm) REVERT: C 113 TYR cc_start: 0.8686 (m-80) cc_final: 0.8374 (m-80) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.3750 time to fit residues: 28.8621 Evaluate side-chains 74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130258 restraints weight = 14687.840| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.14 r_work: 0.3292 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6191 Z= 0.113 Angle : 0.476 13.428 8418 Z= 0.248 Chirality : 0.040 0.138 919 Planarity : 0.003 0.042 1038 Dihedral : 6.132 69.329 959 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.79 % Allowed : 16.40 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 737 helix: 1.60 (0.29), residues: 326 sheet: 0.54 (0.42), residues: 148 loop : -0.73 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.014 0.001 TYR A 414 PHE 0.011 0.001 PHE A 49 TRP 0.011 0.001 TRP A 246 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6189) covalent geometry : angle 0.47613 / 0.25 ( 8414) SS BOND : bond 0.00187 / 0.10 ( 2) SS BOND : angle 0.34888 / 0.19 ( 4) hydrogen bonds : bond 0.03867 / 2.49 ( 323) hydrogen bonds : angle 4.13193 / 3.03 ( 892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.139 Fit side-chains REVERT: A 49 PHE cc_start: 0.7726 (t80) cc_final: 0.7356 (t80) REVERT: A 129 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7249 (mttm) REVERT: A 438 MET cc_start: 0.8025 (mmm) cc_final: 0.7607 (mmm) REVERT: C 113 TYR cc_start: 0.8673 (m-80) cc_final: 0.8353 (m-80) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.3391 time to fit residues: 26.1098 Evaluate side-chains 71 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132417 restraints weight = 20278.638| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.87 r_work: 0.3254 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6191 Z= 0.099 Angle : 0.458 12.552 8418 Z= 0.240 Chirality : 0.040 0.146 919 Planarity : 0.003 0.041 1038 Dihedral : 5.983 69.014 959 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.79 % Allowed : 16.88 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.31), residues: 737 helix: 1.69 (0.29), residues: 326 sheet: 0.56 (0.43), residues: 148 loop : -0.68 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 312 TYR 0.012 0.001 TYR A 414 PHE 0.010 0.001 PHE A 49 TRP 0.010 0.001 TRP A 246 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6189) covalent geometry : angle 0.45854 / 0.24 ( 8414) SS BOND : bond 0.00172 / 0.09 ( 2) SS BOND : angle 0.30366 / 0.16 ( 4) hydrogen bonds : bond 0.03630 / 2.34 ( 323) hydrogen bonds : angle 4.06071 / 2.98 ( 892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.163 Fit side-chains REVERT: A 49 PHE cc_start: 0.7775 (t80) cc_final: 0.7393 (t80) REVERT: A 129 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7276 (mttm) REVERT: A 438 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7451 (mmm) REVERT: C 113 TYR cc_start: 0.8588 (m-80) cc_final: 0.8280 (m-80) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.3741 time to fit residues: 28.0294 Evaluate side-chains 71 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 449 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131786 restraints weight = 17968.309| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.05 r_work: 0.3257 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6191 Z= 0.116 Angle : 0.476 13.420 8418 Z= 0.248 Chirality : 0.040 0.139 919 Planarity : 0.003 0.043 1038 Dihedral : 6.012 69.008 959 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.95 % Allowed : 16.72 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.31), residues: 737 helix: 1.66 (0.29), residues: 326 sheet: 0.57 (0.43), residues: 148 loop : -0.71 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.014 0.001 TYR A 414 PHE 0.011 0.001 PHE A 49 TRP 0.011 0.001 TRP A 287 HIS 0.005 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6189) covalent geometry : angle 0.47637 / 0.25 ( 8414) SS BOND : bond 0.00200 / 0.10 ( 2) SS BOND : angle 0.39499 / 0.21 ( 4) hydrogen bonds : bond 0.03837 / 2.47 ( 323) hydrogen bonds : angle 4.10317 / 3.00 ( 892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.90 seconds wall clock time: 39 minutes 31.25 seconds (2371.25 seconds total)