Starting phenix.real_space_refine on Thu Jul 2 03:00:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yq4_73323/07_2026/9yq4_73323.map" } resolution = 3.3 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= 0.053 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 1 7.51 5 P 2 5.49 5 S 35 5.16 5 C 3866 2.51 5 N 983 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 5993 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4024 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 1 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'UGA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.26 Number of scatterers: 5993 At special positions: 0 Unit cell: (70.2, 95.04, 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 1 24.99 S 35 16.00 P 2 15.00 O 1106 8.00 N 983 7.00 C 3866 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=2.04 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: 0.52 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 43.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 39 through 74 removed outlier: 6.330A pdb=" N VAL A 45 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 70 " --> pdb=" O MET A 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 127 through 136 removed outlier: 5.548A pdb=" N ILE A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.013A pdb=" N GLY A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.638A pdb=" N TYR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix removed outlier: 3.514A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 253 removed outlier: 3.632A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.583A pdb=" N GLN A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 4.603A pdb=" N GLU A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.397A 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: 3.714A pdb=" N ARG A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 364 through 391 removed outlier: 3.502A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 420 removed outlier: 3.758A pdb=" N ALA A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.507A pdb=" N TYR A 426 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.766A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.544A 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 476 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 541 through 549 removed outlier: 4.119A pdb=" N GLU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.628A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.683A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.741A pdb=" N TYR C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.529A pdb=" N GLN A 172 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 230 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP A 325 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.204A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 5.691A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.533A pdb=" N TYR B 113 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.615A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 52 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 762 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: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.49 - 0.79: 1 0.79 - 1.08: 0 1.08 - 1.38: 2279 1.38 - 1.67: 3810 1.67 - 1.97: 56 Warning: very small bond lengths. Bond restraints: 6146 Sorted by residual: bond pdb=" CG PRO A 286 " pdb=" CD PRO A 286 " ideal model delta sigma weight residual 1.503 0.495 1.008 3.40e-02 8.65e+02 8.79e+02 bond pdb=" CB PRO A 286 " pdb=" CG PRO A 286 " ideal model delta sigma weight residual 1.492 1.966 -0.474 5.00e-02 4.00e+02 8.98e+01 bond pdb=" CA PRO A 286 " pdb=" CB PRO A 286 " ideal model delta sigma weight residual 1.534 1.445 0.089 1.79e-02 3.12e+03 2.49e+01 bond pdb=" O5D UGA A 601 " pdb=" PA UGA A 601 " ideal model delta sigma weight residual 1.645 1.741 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" CAI Y01 A 603 " pdb=" CAK Y01 A 603 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 6141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.25: 8348 12.25 - 24.50: 3 24.50 - 36.75: 1 36.75 - 49.00: 0 49.00 - 61.26: 1 Bond angle restraints: 8353 Sorted by residual: angle pdb=" N PRO A 286 " pdb=" CD PRO A 286 " pdb=" CG PRO A 286 " ideal model delta sigma weight residual 103.20 41.94 61.26 1.50e+00 4.44e-01 1.67e+03 angle pdb=" CA PRO A 286 " pdb=" CB PRO A 286 " pdb=" CG PRO A 286 " ideal model delta sigma weight residual 104.50 74.45 30.05 1.90e+00 2.77e-01 2.50e+02 angle pdb=" N PRO A 286 " pdb=" CA PRO A 286 " pdb=" CB PRO A 286 " ideal model delta sigma weight residual 103.20 94.01 9.19 9.50e-01 1.11e+00 9.35e+01 angle pdb=" PA UGA A 601 " pdb=" O3A UGA A 601 " pdb=" PB UGA A 601 " ideal model delta sigma weight residual 123.32 146.56 -23.24 3.00e+00 1.11e-01 6.00e+01 angle pdb=" CB PRO A 286 " pdb=" CG PRO A 286 " pdb=" CD PRO A 286 " ideal model delta sigma weight residual 106.10 84.49 21.61 3.20e+00 9.77e-02 4.56e+01 ... (remaining 8348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 3230 21.39 - 42.78: 336 42.78 - 64.16: 61 64.16 - 85.55: 17 85.55 - 106.94: 6 Dihedral angle restraints: 3650 sinusoidal: 1496 harmonic: 2154 Sorted by residual: dihedral pdb=" CA PRO A 286 " pdb=" CB PRO A 286 " pdb=" CG PRO A 286 " pdb=" CD PRO A 286 " ideal model delta sinusoidal sigma weight residual -38.00 -144.94 106.94 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" CA LYS A 129 " pdb=" C LYS A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR A 289 " pdb=" C THR A 289 " pdb=" N GLN A 290 " pdb=" CA GLN A 290 " ideal model delta harmonic sigma weight residual 180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 3647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 838 0.082 - 0.164: 68 0.164 - 0.246: 3 0.246 - 0.328: 3 0.328 - 0.410: 1 Chirality restraints: 913 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 4.21e+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 2.49 -0.27 2.00e-01 2.50e+01 1.88e+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 1.85e+00 ... (remaining 910 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 104 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" CG ASP B 104 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASP B 104 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP B 104 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 252 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C PHE A 252 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 252 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 253 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 118 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C THR B 118 " -0.041 2.00e-02 2.50e+03 pdb=" O THR B 118 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN B 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 114 2.67 - 3.23: 5575 3.23 - 3.79: 9011 3.79 - 4.34: 12196 4.34 - 4.90: 20701 Nonbonded interactions: 47597 Sorted by model distance: nonbonded pdb=" OE1 GLU A 93 " pdb="MN MN A 602 " model vdw 2.113 3.060 nonbonded pdb=" OH TYR A 432 " pdb=" OH TYR A 517 " model vdw 2.123 3.040 nonbonded pdb=" OD1 ASN A 235 " pdb=" OG SER A 241 " model vdw 2.195 3.040 nonbonded pdb=" ND2 ASN A 167 " pdb=" O ARG C 101 " model vdw 2.204 3.120 nonbonded pdb=" O SER A 165 " pdb=" OG SER C 103 " model vdw 2.229 3.040 ... (remaining 47592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.015 1.008 6148 Z= 0.468 Angle : 1.097 61.256 8357 Z= 0.617 Chirality : 0.050 0.410 913 Planarity : 0.004 0.038 1031 Dihedral : 17.928 106.940 2274 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.16 % Allowed : 20.63 % Favored : 79.21 % 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: -0.77 (0.31), residues: 731 helix: 0.52 (0.31), residues: 294 sheet: -0.19 (0.45), residues: 151 loop : -1.75 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.016 0.001 TYR A 528 PHE 0.024 0.001 PHE A 49 TRP 0.033 0.001 TRP A 346 HIS 0.004 0.002 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.01514 / 0.47 ( 6146) covalent geometry : angle 1.09713 / 0.62 ( 8353) SS BOND : bond 0.00375 / 0.18 ( 2) SS BOND : angle 0.99741 / 0.51 ( 4) hydrogen bonds : bond 0.13837 / 9.23 ( 270) hydrogen bonds : angle 5.39506 / 3.88 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6136 (m-40) cc_final: 0.5926 (m-40) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.0785 time to fit residues: 10.6692 Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139984 restraints weight = 8004.813| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.60 r_work: 0.3380 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6148 Z= 0.139 Angle : 0.547 10.758 8357 Z= 0.294 Chirality : 0.041 0.164 913 Planarity : 0.004 0.036 1031 Dihedral : 10.260 84.777 953 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.22 % Allowed : 21.27 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.32), residues: 731 helix: 0.76 (0.31), residues: 289 sheet: -0.21 (0.44), residues: 161 loop : -1.75 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.015 0.001 TYR A 414 PHE 0.011 0.001 PHE C 47 TRP 0.017 0.001 TRP A 346 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6146) covalent geometry : angle 0.54667 / 0.29 ( 8353) SS BOND : bond 0.00288 / 0.14 ( 2) SS BOND : angle 0.68153 / 0.36 ( 4) hydrogen bonds : bond 0.04014 / 2.77 ( 270) hydrogen bonds : angle 4.36934 / 3.16 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8799 (t0) cc_final: 0.8343 (p0) REVERT: A 495 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8844 (p) REVERT: C 81 GLU cc_start: 0.6963 (mp0) cc_final: 0.6682 (pm20) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.0657 time to fit residues: 10.1785 Evaluate side-chains 108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.168373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144805 restraints weight = 7827.023| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.56 r_work: 0.3412 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6148 Z= 0.149 Angle : 0.530 7.222 8357 Z= 0.285 Chirality : 0.041 0.144 913 Planarity : 0.004 0.039 1031 Dihedral : 9.085 76.630 953 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.49 % Allowed : 20.48 % Favored : 76.03 % 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: -0.64 (0.32), residues: 731 helix: 0.62 (0.31), residues: 289 sheet: -0.12 (0.44), residues: 159 loop : -1.67 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.015 0.001 TYR A 414 PHE 0.011 0.001 PHE C 47 TRP 0.020 0.001 TRP A 346 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6146) covalent geometry : angle 0.52981 / 0.28 ( 8353) SS BOND : bond 0.00294 / 0.14 ( 2) SS BOND : angle 0.71753 / 0.35 ( 4) hydrogen bonds : bond 0.04066 / 2.81 ( 270) hydrogen bonds : angle 4.32357 / 3.15 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6963 (mp) REVERT: A 235 ASN cc_start: 0.8695 (t0) cc_final: 0.8031 (p0) REVERT: A 370 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: A 442 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5972 (mmt180) REVERT: A 495 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 104 ASP cc_start: 0.7794 (p0) cc_final: 0.7531 (p0) REVERT: C 78 MET cc_start: 0.7585 (ptt) cc_final: 0.7343 (ptp) REVERT: C 81 GLU cc_start: 0.6896 (mp0) cc_final: 0.6557 (pm20) REVERT: C 89 ASP cc_start: 0.7896 (t0) cc_final: 0.7439 (t0) outliers start: 22 outliers final: 12 residues processed: 122 average time/residue: 0.0677 time to fit residues: 11.3341 Evaluate side-chains 114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146199 restraints weight = 7862.656| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.61 r_work: 0.3399 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6148 Z= 0.119 Angle : 0.491 6.161 8357 Z= 0.267 Chirality : 0.040 0.145 913 Planarity : 0.004 0.039 1031 Dihedral : 8.154 75.506 953 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.33 % Allowed : 21.90 % Favored : 74.76 % 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: -0.43 (0.32), residues: 731 helix: 0.87 (0.32), residues: 283 sheet: -0.11 (0.44), residues: 159 loop : -1.54 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.015 0.001 TYR A 414 PHE 0.042 0.001 PHE C 47 TRP 0.020 0.001 TRP A 346 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6146) covalent geometry : angle 0.49043 / 0.27 ( 8353) SS BOND : bond 0.00303 / 0.15 ( 2) SS BOND : angle 0.78976 / 0.41 ( 4) hydrogen bonds : bond 0.03715 / 2.58 ( 270) hydrogen bonds : angle 4.20443 / 3.06 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8650 (t0) cc_final: 0.8018 (p0) REVERT: A 237 ASP cc_start: 0.7956 (p0) cc_final: 0.7720 (p0) REVERT: A 370 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: A 495 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8854 (p) REVERT: B 104 ASP cc_start: 0.7688 (p0) cc_final: 0.7425 (p0) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.0665 time to fit residues: 10.7265 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.172020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149546 restraints weight = 7950.799| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.54 r_work: 0.3414 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6148 Z= 0.113 Angle : 0.484 5.858 8357 Z= 0.264 Chirality : 0.040 0.147 913 Planarity : 0.004 0.039 1031 Dihedral : 7.354 77.067 953 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.33 % Allowed : 21.59 % Favored : 75.08 % 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: -0.36 (0.32), residues: 731 helix: 0.96 (0.32), residues: 283 sheet: -0.09 (0.43), residues: 159 loop : -1.52 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.015 0.001 TYR A 414 PHE 0.030 0.001 PHE C 47 TRP 0.023 0.001 TRP A 346 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6146) covalent geometry : angle 0.48353 / 0.26 ( 8353) SS BOND : bond 0.00288 / 0.14 ( 2) SS BOND : angle 0.68738 / 0.34 ( 4) hydrogen bonds : bond 0.03639 / 2.54 ( 270) hydrogen bonds : angle 4.10941 / 2.99 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8623 (t0) cc_final: 0.7969 (p0) REVERT: A 237 ASP cc_start: 0.7943 (p0) cc_final: 0.7726 (p0) REVERT: A 370 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: A 495 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8887 (p) REVERT: B 104 ASP cc_start: 0.7615 (p0) cc_final: 0.7347 (p0) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.0733 time to fit residues: 11.7773 Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.162232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138568 restraints weight = 7960.740| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.57 r_work: 0.3344 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6148 Z= 0.199 Angle : 0.565 5.801 8357 Z= 0.305 Chirality : 0.043 0.195 913 Planarity : 0.004 0.040 1031 Dihedral : 7.442 81.916 953 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.13 % Allowed : 21.43 % Favored : 74.44 % 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: -0.70 (0.31), residues: 731 helix: 0.51 (0.31), residues: 289 sheet: -0.16 (0.43), residues: 162 loop : -1.63 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.018 0.002 TYR A 528 PHE 0.026 0.002 PHE C 47 TRP 0.025 0.002 TRP A 346 HIS 0.005 0.002 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 6146) covalent geometry : angle 0.56463 / 0.30 ( 8353) SS BOND : bond 0.00364 / 0.18 ( 2) SS BOND : angle 0.74274 / 0.36 ( 4) hydrogen bonds : bond 0.04325 / 2.97 ( 270) hydrogen bonds : angle 4.30430 / 3.12 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: A 495 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 104 ASP cc_start: 0.7653 (p0) cc_final: 0.7314 (p0) REVERT: C 89 ASP cc_start: 0.7930 (t0) cc_final: 0.7478 (t0) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 0.0635 time to fit residues: 10.6687 Evaluate side-chains 119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.171733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.148537 restraints weight = 7816.369| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.50 r_work: 0.3402 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6148 Z= 0.116 Angle : 0.491 5.568 8357 Z= 0.267 Chirality : 0.040 0.149 913 Planarity : 0.004 0.039 1031 Dihedral : 6.990 79.833 953 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.49 % Allowed : 22.06 % Favored : 74.44 % 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: -0.39 (0.32), residues: 731 helix: 0.90 (0.32), residues: 283 sheet: -0.01 (0.45), residues: 148 loop : -1.51 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.015 0.001 TYR A 414 PHE 0.040 0.001 PHE C 47 TRP 0.018 0.001 TRP A 346 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6146) covalent geometry : angle 0.49050 / 0.27 ( 8353) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.63684 / 0.32 ( 4) hydrogen bonds : bond 0.03705 / 2.58 ( 270) hydrogen bonds : angle 4.11007 / 2.99 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7555 (tptm) cc_final: 0.7336 (tptm) REVERT: A 235 ASN cc_start: 0.8707 (t0) cc_final: 0.8300 (p0) REVERT: A 237 ASP cc_start: 0.7858 (p0) cc_final: 0.7642 (p0) REVERT: A 370 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: A 495 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 104 ASP cc_start: 0.7528 (p0) cc_final: 0.7229 (p0) REVERT: C 78 MET cc_start: 0.7586 (ptt) cc_final: 0.7370 (ptp) REVERT: C 89 ASP cc_start: 0.7968 (t0) cc_final: 0.7613 (t0) outliers start: 22 outliers final: 17 residues processed: 117 average time/residue: 0.0614 time to fit residues: 9.7177 Evaluate side-chains 115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.175515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.152917 restraints weight = 7818.718| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.47 r_work: 0.3475 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6148 Z= 0.088 Angle : 0.452 5.448 8357 Z= 0.247 Chirality : 0.039 0.146 913 Planarity : 0.003 0.041 1031 Dihedral : 6.342 76.068 953 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.70 % Allowed : 23.02 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.32), residues: 731 helix: 1.01 (0.32), residues: 292 sheet: 0.17 (0.45), residues: 145 loop : -1.48 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.014 0.001 TYR A 414 PHE 0.037 0.001 PHE C 47 TRP 0.032 0.001 TRP A 346 HIS 0.001 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 6146) covalent geometry : angle 0.45195 / 0.25 ( 8353) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 0.56716 / 0.28 ( 4) hydrogen bonds : bond 0.03172 / 2.21 ( 270) hydrogen bonds : angle 3.89191 / 2.83 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8644 (t0) cc_final: 0.8268 (p0) REVERT: A 237 ASP cc_start: 0.7778 (p0) cc_final: 0.7493 (p0) REVERT: A 370 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: C 89 ASP cc_start: 0.7916 (t0) cc_final: 0.7591 (t0) REVERT: C 106 TYR cc_start: 0.8440 (t80) cc_final: 0.7970 (t80) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.0734 time to fit residues: 11.2904 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140482 restraints weight = 7976.680| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.59 r_work: 0.3416 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6148 Z= 0.122 Angle : 0.490 5.327 8357 Z= 0.269 Chirality : 0.041 0.224 913 Planarity : 0.004 0.040 1031 Dihedral : 6.407 76.598 953 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.17 % Allowed : 21.90 % Favored : 74.92 % 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: -0.27 (0.32), residues: 731 helix: 0.90 (0.32), residues: 292 sheet: 0.20 (0.45), residues: 145 loop : -1.47 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.014 0.001 TYR A 414 PHE 0.039 0.001 PHE C 47 TRP 0.028 0.001 TRP A 346 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6146) covalent geometry : angle 0.48999 / 0.27 ( 8353) SS BOND : bond 0.00285 / 0.14 ( 2) SS BOND : angle 0.61287 / 0.30 ( 4) hydrogen bonds : bond 0.03496 / 2.42 ( 270) hydrogen bonds : angle 3.97097 / 2.89 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8695 (t0) cc_final: 0.8278 (p0) REVERT: A 237 ASP cc_start: 0.7879 (p0) cc_final: 0.7608 (p0) REVERT: A 370 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: C 89 ASP cc_start: 0.7886 (t0) cc_final: 0.7585 (t0) REVERT: C 106 TYR cc_start: 0.8478 (t80) cc_final: 0.7993 (t80) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.0704 time to fit residues: 10.4560 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 18 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.166512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140994 restraints weight = 7950.606| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.60 r_work: 0.3426 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6148 Z= 0.101 Angle : 0.471 5.902 8357 Z= 0.257 Chirality : 0.040 0.155 913 Planarity : 0.004 0.040 1031 Dihedral : 6.301 75.695 953 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.38 % Allowed : 23.17 % Favored : 74.44 % 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: -0.21 (0.32), residues: 731 helix: 1.00 (0.32), residues: 292 sheet: 0.17 (0.44), residues: 145 loop : -1.46 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.014 0.001 TYR A 414 PHE 0.038 0.001 PHE C 47 TRP 0.030 0.001 TRP A 346 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6146) covalent geometry : angle 0.47111 / 0.26 ( 8353) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 0.63306 / 0.31 ( 4) hydrogen bonds : bond 0.03334 / 2.32 ( 270) hydrogen bonds : angle 3.90823 / 2.84 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8670 (t0) cc_final: 0.8272 (p0) REVERT: A 237 ASP cc_start: 0.7821 (p0) cc_final: 0.7550 (p0) REVERT: A 370 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: B 82 MET cc_start: 0.6817 (ttm) cc_final: 0.6480 (mtm) REVERT: C 89 ASP cc_start: 0.7908 (t0) cc_final: 0.7621 (t0) REVERT: C 106 TYR cc_start: 0.8462 (t80) cc_final: 0.7994 (t80) outliers start: 15 outliers final: 14 residues processed: 103 average time/residue: 0.0711 time to fit residues: 9.9265 Evaluate side-chains 107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.165649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141236 restraints weight = 8005.049| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.59 r_work: 0.3415 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6148 Z= 0.128 Angle : 0.497 5.576 8357 Z= 0.271 Chirality : 0.041 0.185 913 Planarity : 0.004 0.040 1031 Dihedral : 6.382 76.453 953 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.02 % Allowed : 22.86 % Favored : 74.13 % 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: -0.19 (0.32), residues: 731 helix: 1.05 (0.32), residues: 283 sheet: 0.17 (0.44), residues: 145 loop : -1.41 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.013 0.001 TYR A 414 PHE 0.038 0.001 PHE C 47 TRP 0.030 0.001 TRP A 346 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6146) covalent geometry : angle 0.49672 / 0.27 ( 8353) SS BOND : bond 0.00305 / 0.15 ( 2) SS BOND : angle 0.66826 / 0.32 ( 4) hydrogen bonds : bond 0.03610 / 2.50 ( 270) hydrogen bonds : angle 3.99984 / 2.92 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.56 seconds wall clock time: 26 minutes 47.09 seconds (1607.09 seconds total)