Starting phenix.real_space_refine on Fri Aug 22 16:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snd_40623/08_2025/8snd_40623.map" } resolution = 3.1 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= -0.002 sd= 0.119 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 3 5.49 5 S 35 5.16 5 C 3928 2.51 5 N 992 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} 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: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 138 Unusual residues: {' MN': 2, '3PE': 1, 'NAG': 1, 'UGA': 1, 'Y01': 1} Classifications: {'undetermined': 6, 'water': 8} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 1.32, per 1000 atoms: 0.22 Number of scatterers: 6090 At special positions: 0 Unit cell: (74.52, 75.6, 152.28, 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 3 15.00 O 1130 8.00 N 992 7.00 C 3928 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: 0.39 Conformation dependent library (CDL) restraints added in 242.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 45.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 4.188A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.748A 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 125 through 138 removed outlier: 3.979A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.801A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.534A pdb=" N TRP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.558A pdb=" N ALA A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.992A pdb=" N ILE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 331 through 355 removed outlier: 3.648A pdb=" N SER A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 391 removed outlier: 4.152A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.679A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.930A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 468 through 497 removed outlier: 5.199A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.693A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.925A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 8.679A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 273 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 229 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N ILE A 224 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 16.448A pdb=" N ALA A 226 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 12.541A pdb=" N ALA A 322 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ALA A 228 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLY A 324 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU A 230 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER A 326 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 232 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 5.961A 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 8 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.621A pdb=" N VAL B 12 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.681A 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 removed outlier: 3.814A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.797A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 115 " --> pdb=" O LEU C 97 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 846 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: 0.95 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 943 1.31 - 1.44: 1867 1.44 - 1.56: 3363 1.56 - 1.69: 8 1.69 - 1.81: 53 Bond restraints: 6234 Sorted by residual: bond pdb=" C3D UGA A 603 " pdb=" C4D UGA A 603 " ideal model delta sigma weight residual 1.525 1.266 0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1D UGA A 603 " pdb=" C2D UGA A 603 " ideal model delta sigma weight residual 1.528 1.276 0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1D UGA A 603 " pdb=" O4D UGA A 603 " ideal model delta sigma weight residual 1.393 1.553 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C2D UGA A 603 " pdb=" C3D UGA A 603 " ideal model delta sigma weight residual 1.534 1.659 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C4D UGA A 603 " pdb=" O4D UGA A 603 " ideal model delta sigma weight residual 1.432 1.555 -0.123 2.00e-02 2.50e+03 3.81e+01 ... (remaining 6229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 8430 3.23 - 6.46: 25 6.46 - 9.68: 4 9.68 - 12.91: 2 12.91 - 16.14: 2 Bond angle restraints: 8463 Sorted by residual: angle pdb=" O3A UGA A 603 " pdb=" PA UGA A 603 " pdb=" O5D UGA A 603 " ideal model delta sigma weight residual 93.30 109.44 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3A UGA A 603 " pdb=" PB UGA A 603 " pdb=" O3B UGA A 603 " ideal model delta sigma weight residual 94.34 109.55 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O1A UGA A 603 " pdb=" PA UGA A 603 " pdb=" O2A UGA A 603 " ideal model delta sigma weight residual 120.95 109.55 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B UGA A 603 " pdb=" PB UGA A 603 " pdb=" O2B UGA A 603 " ideal model delta sigma weight residual 120.33 109.29 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ILE A 211 " pdb=" CA ILE A 211 " pdb=" C ILE A 211 " ideal model delta sigma weight residual 111.81 108.79 3.02 8.60e-01 1.35e+00 1.24e+01 ... (remaining 8458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 3317 20.74 - 41.48: 335 41.48 - 62.22: 55 62.22 - 82.96: 16 82.96 - 103.70: 6 Dihedral angle restraints: 3729 sinusoidal: 1567 harmonic: 2162 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 -86.00 -36.87 -49.13 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" O21 3PE A 601 " pdb=" C2 3PE A 601 " pdb=" C3 3PE A 601 " pdb=" O31 3PE A 601 " ideal model delta sinusoidal sigma weight residual 60.47 -43.23 103.70 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CB GLU A 255 " pdb=" CG GLU A 255 " pdb=" CD GLU A 255 " pdb=" OE1 GLU A 255 " ideal model delta sinusoidal sigma weight residual 0.00 89.52 -89.52 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 756 0.051 - 0.102: 139 0.102 - 0.153: 25 0.153 - 0.204: 1 0.204 - 0.255: 2 Chirality restraints: 923 Sorted by residual: chirality pdb=" C3D UGA A 603 " pdb=" C2D UGA A 603 " pdb=" C4D UGA A 603 " pdb=" O3D UGA A 603 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2' UGA A 603 " pdb=" C1' UGA A 603 " pdb=" C3' UGA A 603 " pdb=" O2' UGA A 603 " both_signs ideal model delta sigma weight residual False -2.23 -2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2D UGA A 603 " pdb=" C1D UGA A 603 " pdb=" C3D UGA A 603 " pdb=" O2D UGA A 603 " both_signs ideal model delta sigma weight residual False -2.62 -2.44 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 920 not shown) Planarity restraints: 1038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 40 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 41 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 172 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO A 173 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.016 5.00e-02 4.00e+02 ... (remaining 1035 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1301 2.78 - 3.31: 5501 3.31 - 3.84: 9722 3.84 - 4.37: 11432 4.37 - 4.90: 20464 Nonbonded interactions: 48420 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 605 " model vdw 2.262 2.320 nonbonded pdb=" O ALA B 24 " pdb=" ND2 ASN B 76 " model vdw 2.297 3.120 nonbonded pdb=" NE2 GLN A 338 " pdb=" O2B UGA A 603 " model vdw 2.309 3.120 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 71 " model vdw 2.324 3.120 ... (remaining 48415 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: 1.180 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.860 Find NCS groups from input model: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.007 0.259 6236 Z= 0.337 Angle : 0.595 16.141 8467 Z= 0.290 Chirality : 0.042 0.255 923 Planarity : 0.003 0.035 1038 Dihedral : 17.167 103.702 2347 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.64 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % 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 aren not related in a simple way. whole: 1.20 (0.31), residues: 732 helix: 1.67 (0.30), residues: 311 sheet: 1.43 (0.40), residues: 161 loop : -0.70 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.015 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.013 0.001 TRP A 41 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 6234) covalent geometry : angle 0.59491 ( 8463) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.84019 ( 4) hydrogen bonds : bond 0.13669 ( 303) hydrogen bonds : angle 5.07342 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 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: 0 poor density : 76 time to evaluate : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0615 time to fit residues: 6.4538 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133166 restraints weight = 6755.051| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.43 r_work: 0.3427 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6236 Z= 0.212 Angle : 0.541 5.226 8467 Z= 0.291 Chirality : 0.044 0.172 923 Planarity : 0.004 0.050 1038 Dihedral : 8.978 91.877 1019 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 2.69 % Allowed : 16.61 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.31), residues: 732 helix: 1.49 (0.30), residues: 309 sheet: 1.04 (0.40), residues: 165 loop : -0.64 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.012 0.002 TYR A 414 PHE 0.014 0.002 PHE B 47 TRP 0.014 0.001 TRP A 472 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 6234) covalent geometry : angle 0.54118 ( 8463) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.75955 ( 4) hydrogen bonds : bond 0.05302 ( 303) hydrogen bonds : angle 4.20490 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.207 Fit side-chains REVERT: A 124 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 438 MET cc_start: 0.7629 (mtp) cc_final: 0.7366 (mtp) outliers start: 17 outliers final: 13 residues processed: 97 average time/residue: 0.0572 time to fit residues: 7.6889 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 32 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138155 restraints weight = 6664.453| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.34 r_work: 0.3498 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6236 Z= 0.102 Angle : 0.428 5.082 8467 Z= 0.234 Chirality : 0.040 0.156 923 Planarity : 0.003 0.051 1038 Dihedral : 8.302 85.694 1019 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.81 % Rotamer: Outliers : 3.80 % Allowed : 16.30 % Favored : 79.91 % 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 aren not related in a simple way. whole: 1.20 (0.31), residues: 732 helix: 1.90 (0.30), residues: 305 sheet: 1.03 (0.40), residues: 165 loop : -0.67 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 71 TYR 0.010 0.001 TYR A 414 PHE 0.011 0.001 PHE C 69 TRP 0.007 0.001 TRP A 472 HIS 0.001 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6234) covalent geometry : angle 0.42821 ( 8463) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.42854 ( 4) hydrogen bonds : bond 0.03771 ( 303) hydrogen bonds : angle 3.85385 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.178 Fit side-chains REVERT: A 350 ILE cc_start: 0.7755 (tp) cc_final: 0.7226 (tp) outliers start: 24 outliers final: 17 residues processed: 99 average time/residue: 0.0580 time to fit residues: 8.0042 Evaluate side-chains 92 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140501 restraints weight = 6729.077| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.28 r_work: 0.3519 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6236 Z= 0.131 Angle : 0.444 5.213 8467 Z= 0.242 Chirality : 0.040 0.161 923 Planarity : 0.003 0.053 1038 Dihedral : 8.326 83.069 1019 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 4.27 % Allowed : 16.61 % Favored : 79.11 % 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 aren not related in a simple way. whole: 1.17 (0.31), residues: 732 helix: 1.94 (0.31), residues: 305 sheet: 1.05 (0.42), residues: 155 loop : -0.75 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.010 0.001 TYR A 414 PHE 0.011 0.001 PHE B 47 TRP 0.009 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6234) covalent geometry : angle 0.44366 ( 8463) SS BOND : bond 0.00313 ( 2) SS BOND : angle 0.45686 ( 4) hydrogen bonds : bond 0.04006 ( 303) hydrogen bonds : angle 3.84445 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.173 Fit side-chains REVERT: A 62 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7263 (tt0) REVERT: A 438 MET cc_start: 0.7516 (mtp) cc_final: 0.7263 (mtp) REVERT: B 105 TYR cc_start: 0.8918 (p90) cc_final: 0.8692 (p90) outliers start: 27 outliers final: 21 residues processed: 102 average time/residue: 0.0599 time to fit residues: 8.3839 Evaluate side-chains 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141196 restraints weight = 6857.448| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.30 r_work: 0.3544 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6236 Z= 0.119 Angle : 0.440 5.139 8467 Z= 0.239 Chirality : 0.040 0.160 923 Planarity : 0.003 0.053 1038 Dihedral : 8.246 83.640 1019 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 4.27 % Allowed : 16.77 % Favored : 78.96 % 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 aren not related in a simple way. whole: 1.20 (0.32), residues: 732 helix: 1.93 (0.31), residues: 306 sheet: 1.03 (0.40), residues: 165 loop : -0.73 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.010 0.001 TYR A 550 PHE 0.011 0.001 PHE B 47 TRP 0.009 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6234) covalent geometry : angle 0.43985 ( 8463) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.24608 ( 4) hydrogen bonds : bond 0.03801 ( 303) hydrogen bonds : angle 3.79965 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.171 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 101 average time/residue: 0.0619 time to fit residues: 8.5442 Evaluate side-chains 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143536 restraints weight = 6696.484| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.25 r_work: 0.3547 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6236 Z= 0.109 Angle : 0.429 5.146 8467 Z= 0.234 Chirality : 0.040 0.156 923 Planarity : 0.003 0.053 1038 Dihedral : 8.092 84.631 1019 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.32 % Favored : 97.54 % Rotamer: Outliers : 3.96 % Allowed : 17.56 % Favored : 78.48 % 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 aren not related in a simple way. whole: 1.27 (0.32), residues: 732 helix: 2.03 (0.30), residues: 305 sheet: 1.05 (0.41), residues: 165 loop : -0.73 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.015 0.001 TYR B 105 PHE 0.011 0.001 PHE B 47 TRP 0.008 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6234) covalent geometry : angle 0.42890 ( 8463) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.50037 ( 4) hydrogen bonds : bond 0.03590 ( 303) hydrogen bonds : angle 3.74685 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.228 Fit side-chains REVERT: A 62 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7318 (tt0) outliers start: 25 outliers final: 20 residues processed: 98 average time/residue: 0.0599 time to fit residues: 8.1455 Evaluate side-chains 99 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR 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 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 15 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142527 restraints weight = 6801.164| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.34 r_work: 0.3552 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6236 Z= 0.102 Angle : 0.419 5.075 8467 Z= 0.229 Chirality : 0.040 0.156 923 Planarity : 0.003 0.052 1038 Dihedral : 7.974 85.699 1019 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 3.80 % Allowed : 17.72 % Favored : 78.48 % 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 aren not related in a simple way. whole: 1.31 (0.32), residues: 732 helix: 2.09 (0.31), residues: 305 sheet: 1.06 (0.41), residues: 165 loop : -0.74 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 348 TYR 0.014 0.001 TYR B 105 PHE 0.010 0.001 PHE B 47 TRP 0.008 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6234) covalent geometry : angle 0.41894 ( 8463) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.64597 ( 4) hydrogen bonds : bond 0.03436 ( 303) hydrogen bonds : angle 3.70666 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.151 Fit side-chains REVERT: A 62 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7158 (tt0) REVERT: A 426 TYR cc_start: 0.8489 (m-10) cc_final: 0.7891 (m-10) outliers start: 24 outliers final: 23 residues processed: 100 average time/residue: 0.0682 time to fit residues: 9.2748 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR 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 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140567 restraints weight = 6745.072| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.31 r_work: 0.3529 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6236 Z= 0.129 Angle : 0.442 5.129 8467 Z= 0.241 Chirality : 0.041 0.160 923 Planarity : 0.003 0.053 1038 Dihedral : 8.040 85.962 1019 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.32 % Favored : 97.54 % Rotamer: Outliers : 3.80 % Allowed : 18.35 % Favored : 77.85 % 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 aren not related in a simple way. whole: 1.23 (0.32), residues: 732 helix: 2.00 (0.31), residues: 305 sheet: 1.04 (0.41), residues: 165 loop : -0.77 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.012 0.001 TYR B 105 PHE 0.012 0.001 PHE B 47 TRP 0.011 0.001 TRP A 472 HIS 0.001 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6234) covalent geometry : angle 0.44155 ( 8463) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.57507 ( 4) hydrogen bonds : bond 0.03852 ( 303) hydrogen bonds : angle 3.79299 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.192 Fit side-chains REVERT: A 124 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 348 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6989 (ptp90) REVERT: A 426 TYR cc_start: 0.8508 (m-10) cc_final: 0.7894 (m-10) outliers start: 24 outliers final: 22 residues processed: 99 average time/residue: 0.0706 time to fit residues: 9.5876 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140757 restraints weight = 6803.078| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.32 r_work: 0.3521 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6236 Z= 0.123 Angle : 0.447 6.338 8467 Z= 0.243 Chirality : 0.040 0.159 923 Planarity : 0.003 0.053 1038 Dihedral : 7.983 86.018 1019 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.32 % Favored : 97.54 % Rotamer: Outliers : 3.64 % Allowed : 18.99 % Favored : 77.37 % 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 aren not related in a simple way. whole: 1.22 (0.32), residues: 732 helix: 2.00 (0.31), residues: 305 sheet: 1.02 (0.40), residues: 165 loop : -0.78 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 348 TYR 0.014 0.001 TYR B 105 PHE 0.012 0.001 PHE B 47 TRP 0.010 0.001 TRP A 472 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6234) covalent geometry : angle 0.44650 ( 8463) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.45279 ( 4) hydrogen bonds : bond 0.03732 ( 303) hydrogen bonds : angle 3.77490 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.127 Fit side-chains REVERT: A 124 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 426 TYR cc_start: 0.8505 (m-10) cc_final: 0.7901 (m-10) outliers start: 23 outliers final: 22 residues processed: 96 average time/residue: 0.0623 time to fit residues: 8.1934 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140558 restraints weight = 6805.242| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.34 r_work: 0.3518 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6236 Z= 0.126 Angle : 0.444 5.111 8467 Z= 0.243 Chirality : 0.040 0.160 923 Planarity : 0.003 0.053 1038 Dihedral : 7.958 86.306 1019 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 3.48 % Allowed : 18.67 % Favored : 77.85 % 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 aren not related in a simple way. whole: 1.21 (0.32), residues: 732 helix: 1.99 (0.31), residues: 305 sheet: 1.01 (0.40), residues: 165 loop : -0.77 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.014 0.001 TYR B 105 PHE 0.012 0.001 PHE B 47 TRP 0.010 0.001 TRP A 472 HIS 0.001 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6234) covalent geometry : angle 0.44447 ( 8463) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.45231 ( 4) hydrogen bonds : bond 0.03779 ( 303) hydrogen bonds : angle 3.77556 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.192 Fit side-chains REVERT: A 426 TYR cc_start: 0.8506 (m-10) cc_final: 0.7904 (m-10) outliers start: 22 outliers final: 22 residues processed: 96 average time/residue: 0.0590 time to fit residues: 7.8820 Evaluate side-chains 99 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.0980 chunk 17 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143400 restraints weight = 6788.782| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.31 r_work: 0.3554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6236 Z= 0.093 Angle : 0.422 5.059 8467 Z= 0.230 Chirality : 0.039 0.154 923 Planarity : 0.003 0.053 1038 Dihedral : 7.771 87.658 1019 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.91 % Favored : 97.95 % Rotamer: Outliers : 3.01 % Allowed : 19.30 % Favored : 77.69 % 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 aren not related in a simple way. whole: 1.32 (0.32), residues: 732 helix: 2.11 (0.31), residues: 306 sheet: 1.07 (0.40), residues: 165 loop : -0.76 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.017 0.001 TYR B 105 PHE 0.010 0.001 PHE A 49 TRP 0.007 0.001 TRP A 41 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 6234) covalent geometry : angle 0.42178 ( 8463) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.32888 ( 4) hydrogen bonds : bond 0.03226 ( 303) hydrogen bonds : angle 3.65621 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1217.75 seconds wall clock time: 21 minutes 31.42 seconds (1291.42 seconds total)