Starting phenix.real_space_refine on Thu Jul 2 10:08:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvr_17971/07_2026/8pvr_17971.map" } resolution = 3.06 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 C 5426 2.51 5 N 1280 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 8188 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4047 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 18, 'TRANS': 490} Chain breaks: 1 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A Time building chain proxies: 3.19, per 1000 atoms: 0.39 Number of scatterers: 8188 At special positions: 0 Unit cell: (75.0442, 110.13, 88.6886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 6 15.00 O 1422 8.00 N 1280 7.00 C 5426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.71 Conformation dependent library (CDL) restraints added in 468.4 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 1 sheets defined 72.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 19 through 44 removed outlier: 3.792A pdb=" N GLU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.536A pdb=" N VAL B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.857A pdb=" N ILE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 192 removed outlier: 4.359A pdb=" N THR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 171 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 257 removed outlier: 3.515A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 303 Processing helix chain 'B' and resid 304 through 307 removed outlier: 3.902A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 308 through 330 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.710A pdb=" N ALA B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 354 through 381 removed outlier: 4.010A pdb=" N MET B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.646A pdb=" N ILE B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Proline residue: B 414 - end of helix removed outlier: 3.817A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.875A pdb=" N PHE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 487 removed outlier: 3.839A pdb=" N TRP B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.551A pdb=" N MET B 527 " --> pdb=" O TRP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.849A pdb=" N ILE B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 44 removed outlier: 3.793A pdb=" N GLU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 68 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.536A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.858A pdb=" N ILE A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 192 removed outlier: 4.359A pdb=" N THR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 257 removed outlier: 3.515A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 303 Processing helix chain 'A' and resid 304 through 307 removed outlier: 3.902A pdb=" N GLU A 307 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 330 Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.711A pdb=" N ALA A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 354 through 381 removed outlier: 4.010A pdb=" N MET A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 422 removed outlier: 3.646A pdb=" N ILE A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Proline residue: A 414 - end of helix removed outlier: 3.817A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.874A pdb=" N PHE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 487 removed outlier: 3.839A pdb=" N TRP A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR A 481 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.551A pdb=" N MET A 527 " --> pdb=" O TRP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.849A pdb=" N ILE A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 97 removed outlier: 3.988A pdb=" N ARG A 108 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS B 105 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A 106 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS B 107 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR A 104 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU B 109 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR A 102 " --> pdb=" O GLU B 109 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1226 1.31 - 1.44: 2506 1.44 - 1.56: 4594 1.56 - 1.69: 8 1.69 - 1.82: 90 Bond restraints: 8424 Sorted by residual: bond pdb=" O3 EUJ A 601 " pdb=" P3 EUJ A 601 " ideal model delta sigma weight residual 1.727 1.648 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" O3 EUJ B 601 " pdb=" P3 EUJ B 601 " ideal model delta sigma weight residual 1.727 1.648 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1B EUJ B 601 " pdb=" O3C EUJ B 601 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1B EUJ A 601 " pdb=" O3C EUJ A 601 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1A EUJ A 601 " pdb=" O2C EUJ A 601 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 8419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11276 2.46 - 4.91: 110 4.91 - 7.37: 36 7.37 - 9.83: 12 9.83 - 12.28: 4 Bond angle restraints: 11438 Sorted by residual: angle pdb=" O11 EUJ B 601 " pdb=" P1 EUJ B 601 " pdb=" O12 EUJ B 601 " ideal model delta sigma weight residual 121.88 109.60 12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" O11 EUJ A 601 " pdb=" P1 EUJ A 601 " pdb=" O12 EUJ A 601 " ideal model delta sigma weight residual 121.88 109.60 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CB MET A 188 " pdb=" CG MET A 188 " pdb=" SD MET A 188 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET B 188 " pdb=" CG MET B 188 " pdb=" SD MET B 188 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C HIS B 154 " pdb=" CA HIS B 154 " pdb=" CB HIS B 154 " ideal model delta sigma weight residual 115.89 111.20 4.69 1.32e+00 5.74e-01 1.26e+01 ... (remaining 11433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 4517 27.34 - 54.67: 329 54.67 - 82.01: 36 82.01 - 109.34: 8 109.34 - 136.68: 6 Dihedral angle restraints: 4896 sinusoidal: 1950 harmonic: 2946 Sorted by residual: dihedral pdb=" C3B EUJ B 601 " pdb=" C4B EUJ B 601 " pdb=" C5B EUJ B 601 " pdb=" C6B EUJ B 601 " ideal model delta sinusoidal sigma weight residual 163.89 -59.43 -136.68 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3B EUJ A 601 " pdb=" C4B EUJ A 601 " pdb=" C5B EUJ A 601 " pdb=" C6B EUJ A 601 " ideal model delta sinusoidal sigma weight residual 163.89 -59.47 -136.64 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3A EUJ A 601 " pdb=" C4A EUJ A 601 " pdb=" C5A EUJ A 601 " pdb=" C6A EUJ A 601 " ideal model delta sinusoidal sigma weight residual 184.07 59.60 124.47 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1193 0.071 - 0.142: 87 0.142 - 0.213: 2 0.213 - 0.284: 2 0.284 - 0.355: 2 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C2C EUJ B 601 " pdb=" C1C EUJ B 601 " pdb=" C3C EUJ B 601 " pdb=" O2C EUJ B 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.51 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2C EUJ A 601 " pdb=" C1C EUJ A 601 " pdb=" C3C EUJ A 601 " pdb=" O2C EUJ A 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.51 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C5 EUJ B 601 " pdb=" C4 EUJ B 601 " pdb=" C6 EUJ B 601 " pdb=" O5 EUJ B 601 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1283 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 140 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO B 141 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 140 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO A 141 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 139 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 140 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " -0.016 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2053 2.79 - 3.32: 8024 3.32 - 3.85: 13594 3.85 - 4.37: 14343 4.37 - 4.90: 25335 Nonbonded interactions: 63349 Sorted by model distance: nonbonded pdb=" O PHE B 476 " pdb=" OG1 THR B 480 " model vdw 2.268 3.040 nonbonded pdb=" O PHE A 476 " pdb=" OG1 THR A 480 " model vdw 2.268 3.040 nonbonded pdb=" O ALA B 247 " pdb=" OG1 THR B 251 " model vdw 2.354 3.040 nonbonded pdb=" O ALA A 247 " pdb=" OG1 THR A 251 " model vdw 2.355 3.040 nonbonded pdb=" O THR A 70 " pdb=" OG1 THR A 70 " model vdw 2.385 3.040 ... (remaining 63344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.400 Find NCS groups from input model: 0.060 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8424 Z= 0.162 Angle : 0.709 12.281 11438 Z= 0.314 Chirality : 0.040 0.355 1286 Planarity : 0.003 0.033 1406 Dihedral : 19.070 136.680 3004 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.12 % Allowed : 27.96 % Favored : 71.93 % 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: 1.32 (0.27), residues: 1010 helix: 1.91 (0.19), residues: 702 sheet: 1.35 (0.94), residues: 24 loop : -1.92 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.003 0.000 TYR B 148 PHE 0.020 0.001 PHE B 401 TRP 0.005 0.001 TRP B 39 HIS 0.001 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 8424) covalent geometry : angle 0.70882 / 0.31 (11438) hydrogen bonds : bond 0.10419 / 7.41 ( 533) hydrogen bonds : angle 3.95148 / 2.77 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.312 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.0646 time to fit residues: 6.9370 Evaluate side-chains 67 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS A 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.105956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077889 restraints weight = 23666.230| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.79 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8424 Z= 0.100 Angle : 0.466 7.019 11438 Z= 0.244 Chirality : 0.037 0.132 1286 Planarity : 0.003 0.033 1406 Dihedral : 11.692 93.311 1216 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.74 % Allowed : 23.67 % Favored : 74.59 % 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: 1.89 (0.27), residues: 1010 helix: 2.35 (0.20), residues: 708 sheet: 1.32 (0.94), residues: 24 loop : -1.82 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.005 0.001 TYR A 68 PHE 0.012 0.001 PHE A 316 TRP 0.004 0.000 TRP A 39 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 ( 8424) covalent geometry : angle 0.46599 / 0.24 (11438) hydrogen bonds : bond 0.03765 / 2.56 ( 533) hydrogen bonds : angle 3.51544 / 2.45 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.309 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.0585 time to fit residues: 8.0646 Evaluate side-chains 80 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.0270 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.106287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077711 restraints weight = 23340.019| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.75 r_work: 0.3137 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8424 Z= 0.094 Angle : 0.459 7.794 11438 Z= 0.238 Chirality : 0.037 0.141 1286 Planarity : 0.003 0.034 1406 Dihedral : 10.236 88.896 1214 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.55 % Allowed : 22.74 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.28), residues: 1010 helix: 2.45 (0.20), residues: 712 sheet: 1.43 (0.96), residues: 24 loop : -1.91 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 153 TYR 0.005 0.001 TYR A 379 PHE 0.011 0.001 PHE B 134 TRP 0.004 0.000 TRP A 39 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 ( 8424) covalent geometry : angle 0.45930 / 0.24 (11438) hydrogen bonds : bond 0.03424 / 2.32 ( 533) hydrogen bonds : angle 3.40744 / 2.38 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.309 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 0.0628 time to fit residues: 9.2661 Evaluate side-chains 81 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 33 optimal weight: 0.0870 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.2760 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.101763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073698 restraints weight = 23918.582| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.75 r_work: 0.3019 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8424 Z= 0.129 Angle : 0.510 8.693 11438 Z= 0.266 Chirality : 0.039 0.143 1286 Planarity : 0.003 0.032 1406 Dihedral : 9.825 82.983 1214 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.32 % Allowed : 23.32 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.28), residues: 1010 helix: 2.51 (0.20), residues: 710 sheet: 1.51 (0.98), residues: 24 loop : -1.90 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.009 0.001 TYR A 58 PHE 0.015 0.001 PHE B 316 TRP 0.007 0.001 TRP B 474 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8424) covalent geometry : angle 0.51046 / 0.27 (11438) hydrogen bonds : bond 0.04532 / 3.10 ( 533) hydrogen bonds : angle 3.57008 / 2.50 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.315 Fit side-chains REVERT: B 356 ASP cc_start: 0.8529 (t0) cc_final: 0.8313 (t0) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.0661 time to fit residues: 7.9688 Evaluate side-chains 70 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.102544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074858 restraints weight = 23635.338| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.73 r_work: 0.3055 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8424 Z= 0.111 Angle : 0.484 7.406 11438 Z= 0.253 Chirality : 0.038 0.150 1286 Planarity : 0.003 0.033 1406 Dihedral : 9.420 82.717 1214 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 23.67 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.28), residues: 1010 helix: 2.50 (0.20), residues: 710 sheet: 1.68 (0.98), residues: 24 loop : -1.91 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.005 0.001 TYR A 58 PHE 0.013 0.001 PHE A 316 TRP 0.007 0.001 TRP B 39 HIS 0.002 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8424) covalent geometry : angle 0.48412 / 0.25 (11438) hydrogen bonds : bond 0.04048 / 2.76 ( 533) hydrogen bonds : angle 3.53228 / 2.48 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.292 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 75 average time/residue: 0.0627 time to fit residues: 7.5074 Evaluate side-chains 71 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.103151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075320 restraints weight = 23236.893| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.71 r_work: 0.3037 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8424 Z= 0.103 Angle : 0.477 7.633 11438 Z= 0.249 Chirality : 0.038 0.157 1286 Planarity : 0.003 0.033 1406 Dihedral : 9.062 83.304 1214 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.62 % Allowed : 24.25 % 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: 2.08 (0.28), residues: 1010 helix: 2.52 (0.20), residues: 710 sheet: 1.75 (0.98), residues: 24 loop : -1.92 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.005 0.001 TYR A 58 PHE 0.013 0.001 PHE B 316 TRP 0.006 0.000 TRP B 39 HIS 0.002 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 8424) covalent geometry : angle 0.47724 / 0.25 (11438) hydrogen bonds : bond 0.03840 / 2.61 ( 533) hydrogen bonds : angle 3.48480 / 2.45 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.317 Fit side-chains REVERT: B 194 LEU cc_start: 0.8404 (pt) cc_final: 0.8117 (pp) REVERT: A 194 LEU cc_start: 0.8382 (pt) cc_final: 0.8091 (pp) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.0693 time to fit residues: 7.9306 Evaluate side-chains 70 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 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 = 0.3805 r_free = 0.3805 target = 0.103016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073975 restraints weight = 23530.583| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.70 r_work: 0.3065 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8424 Z= 0.105 Angle : 0.475 7.800 11438 Z= 0.249 Chirality : 0.038 0.159 1286 Planarity : 0.003 0.033 1406 Dihedral : 8.809 84.923 1214 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.62 % Allowed : 24.71 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.28), residues: 1010 helix: 2.51 (0.20), residues: 710 sheet: 1.79 (0.98), residues: 24 loop : -1.87 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.005 0.001 TYR A 58 PHE 0.013 0.001 PHE B 316 TRP 0.006 0.001 TRP A 39 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8424) covalent geometry : angle 0.47467 / 0.25 (11438) hydrogen bonds : bond 0.03860 / 2.63 ( 533) hydrogen bonds : angle 3.48840 / 2.45 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.313 Fit side-chains REVERT: B 194 LEU cc_start: 0.8342 (pt) cc_final: 0.8051 (pp) REVERT: A 194 LEU cc_start: 0.8295 (pt) cc_final: 0.8013 (pp) outliers start: 14 outliers final: 14 residues processed: 74 average time/residue: 0.0621 time to fit residues: 7.3367 Evaluate side-chains 72 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.103854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074839 restraints weight = 23302.442| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.78 r_work: 0.3077 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8424 Z= 0.100 Angle : 0.469 8.015 11438 Z= 0.245 Chirality : 0.038 0.162 1286 Planarity : 0.003 0.034 1406 Dihedral : 8.483 87.870 1214 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.62 % Allowed : 24.83 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.28), residues: 1010 helix: 2.51 (0.20), residues: 710 sheet: 1.82 (0.99), residues: 24 loop : -1.83 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.004 0.000 TYR A 58 PHE 0.012 0.001 PHE B 316 TRP 0.005 0.000 TRP A 39 HIS 0.002 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 8424) covalent geometry : angle 0.46928 / 0.25 (11438) hydrogen bonds : bond 0.03660 / 2.49 ( 533) hydrogen bonds : angle 3.44943 / 2.43 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.322 Fit side-chains REVERT: B 194 LEU cc_start: 0.8248 (pt) cc_final: 0.7882 (pp) REVERT: B 436 MET cc_start: 0.9170 (tpt) cc_final: 0.8742 (tpt) REVERT: A 194 LEU cc_start: 0.8251 (pt) cc_final: 0.7931 (pp) REVERT: A 436 MET cc_start: 0.9184 (tpt) cc_final: 0.8757 (tpt) outliers start: 14 outliers final: 14 residues processed: 78 average time/residue: 0.0634 time to fit residues: 7.9046 Evaluate side-chains 75 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 62 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0964 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.102873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073363 restraints weight = 23556.836| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.78 r_work: 0.3071 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8424 Z= 0.117 Angle : 0.486 7.939 11438 Z= 0.255 Chirality : 0.038 0.158 1286 Planarity : 0.003 0.033 1406 Dihedral : 8.400 89.117 1214 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.62 % Allowed : 24.83 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.28), residues: 1010 helix: 2.63 (0.20), residues: 698 sheet: 1.80 (0.99), residues: 24 loop : -1.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.007 0.001 TYR B 58 PHE 0.014 0.001 PHE B 316 TRP 0.005 0.001 TRP B 39 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 8424) covalent geometry : angle 0.48569 / 0.25 (11438) hydrogen bonds : bond 0.04205 / 2.87 ( 533) hydrogen bonds : angle 3.53282 / 2.48 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.316 Fit side-chains REVERT: B 194 LEU cc_start: 0.8406 (pt) cc_final: 0.8089 (pp) REVERT: A 194 LEU cc_start: 0.8504 (pt) cc_final: 0.8246 (pp) outliers start: 14 outliers final: 14 residues processed: 75 average time/residue: 0.0624 time to fit residues: 7.5443 Evaluate side-chains 74 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.103604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074740 restraints weight = 23414.509| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.76 r_work: 0.3093 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8424 Z= 0.106 Angle : 0.492 7.773 11438 Z= 0.257 Chirality : 0.038 0.168 1286 Planarity : 0.003 0.033 1406 Dihedral : 8.270 90.403 1214 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.62 % Allowed : 24.94 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.28), residues: 1010 helix: 2.62 (0.20), residues: 698 sheet: 1.86 (0.98), residues: 24 loop : -1.91 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.005 0.001 TYR A 58 PHE 0.013 0.001 PHE B 316 TRP 0.006 0.001 TRP B 39 HIS 0.002 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8424) covalent geometry : angle 0.49182 / 0.26 (11438) hydrogen bonds : bond 0.03867 / 2.63 ( 533) hydrogen bonds : angle 3.48440 / 2.45 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.312 Fit side-chains REVERT: B 194 LEU cc_start: 0.8389 (pt) cc_final: 0.8080 (pp) REVERT: B 436 MET cc_start: 0.9151 (tpt) cc_final: 0.8745 (tpt) REVERT: A 194 LEU cc_start: 0.8467 (pt) cc_final: 0.8181 (pp) REVERT: A 436 MET cc_start: 0.9150 (tpt) cc_final: 0.8744 (tpt) outliers start: 14 outliers final: 14 residues processed: 73 average time/residue: 0.0631 time to fit residues: 7.3858 Evaluate side-chains 73 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.102959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073410 restraints weight = 23503.662| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.76 r_work: 0.3069 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8424 Z= 0.116 Angle : 0.499 7.521 11438 Z= 0.262 Chirality : 0.038 0.165 1286 Planarity : 0.003 0.033 1406 Dihedral : 8.235 90.289 1214 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.74 % Allowed : 24.94 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.28), residues: 1010 helix: 2.62 (0.20), residues: 698 sheet: 1.90 (0.98), residues: 24 loop : -1.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.007 0.001 TYR B 58 PHE 0.014 0.001 PHE B 316 TRP 0.006 0.001 TRP B 39 HIS 0.003 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 8424) covalent geometry : angle 0.49925 / 0.26 (11438) hydrogen bonds : bond 0.04171 / 2.85 ( 533) hydrogen bonds : angle 3.52581 / 2.48 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.65 seconds wall clock time: 34 minutes 17.11 seconds (2057.11 seconds total)