Starting phenix.real_space_refine on Thu Aug 6 01:54:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275.map" model { file = "/net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqs_65275/08_2026/9vqs_65275_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 8368 2.51 5 N 2024 2.21 5 O 2201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12706 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3097 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "D" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Time building chain proxies: 3.14, per 1000 atoms: 0.25 Number of scatterers: 12706 At special positions: 0 Unit cell: (116.25, 114.39, 112.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 2201 8.00 N 2024 7.00 C 8368 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: 1.04 Conformation dependent library (CDL) restraints added in 583.9 milliseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3026 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 81.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 9 through 27 removed outlier: 3.660A pdb=" N PHE A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 Processing helix chain 'A' and resid 71 through 97 removed outlier: 4.489A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 3.728A pdb=" N GLY A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 162 removed outlier: 3.678A pdb=" N GLU A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Proline residue: A 143 - end of helix Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 180 through 237 removed outlier: 3.887A pdb=" N GLY A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 293 removed outlier: 5.254A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 333 removed outlier: 3.506A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 340 through 357 removed outlier: 3.731A pdb=" N ILE A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 Processing helix chain 'B' and resid 11 through 17 removed outlier: 3.734A pdb=" N ALA B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 38 through 67 Processing helix chain 'B' and resid 70 through 97 removed outlier: 3.868A pdb=" N CYS B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 154 removed outlier: 3.609A pdb=" N THR B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 246 removed outlier: 3.568A pdb=" N MET B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.699A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 378 removed outlier: 5.410A pdb=" N ALA B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 425 removed outlier: 3.949A pdb=" N PHE B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 460 through 482 Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.709A pdb=" N ALA C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 38 through 67 Processing helix chain 'C' and resid 70 through 97 removed outlier: 3.883A pdb=" N CYS C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 117 through 153 removed outlier: 3.574A pdb=" N MET C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 192 through 246 removed outlier: 3.659A pdb=" N MET C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.853A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 378 removed outlier: 5.417A pdb=" N ALA C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 425 removed outlier: 3.848A pdb=" N PHE C 407 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 460 through 482 Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.623A pdb=" N ALA D 15 " --> pdb=" O THR D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 38 through 67 Processing helix chain 'D' and resid 70 through 97 removed outlier: 3.920A pdb=" N CYS D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 107 through 110 removed outlier: 4.387A pdb=" N GLN D 110 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 117 through 153 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 191 through 246 removed outlier: 3.514A pdb=" N TYR D 195 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET D 196 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 324 through 378 removed outlier: 5.287A pdb=" N ALA D 357 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA D 358 " --> pdb=" O THR D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 424 removed outlier: 3.862A pdb=" N PHE D 407 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N MET D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.531A pdb=" N LYS D 447 " --> pdb=" O GLN D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.547A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AA4, first strand: chain 'D' and resid 160 through 165 Processing sheet with id=AA5, first strand: chain 'D' and resid 451 through 452 removed outlier: 4.837A pdb=" N ILE D 451 " --> pdb=" O VAL D 459 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3177 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: 2.19 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3810 1.34 - 1.46: 2391 1.46 - 1.58: 6627 1.58 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 13018 Sorted by residual: bond pdb=" CA MET A 386 " pdb=" C MET A 386 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.27e-02 6.20e+03 2.46e+00 bond pdb=" C ILE A 166 " pdb=" O ILE A 166 " ideal model delta sigma weight residual 1.236 1.220 0.015 1.01e-02 9.80e+03 2.29e+00 bond pdb=" CA SER C 38 " pdb=" C SER C 38 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.26e-02 6.30e+03 1.93e+00 bond pdb=" CA THR A 94 " pdb=" C THR A 94 " ideal model delta sigma weight residual 1.523 1.540 -0.016 1.30e-02 5.92e+03 1.57e+00 bond pdb=" C ILE B 107 " pdb=" O ILE B 107 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.17e-02 7.31e+03 1.51e+00 ... (remaining 13013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 17328 1.54 - 3.08: 254 3.08 - 4.62: 59 4.62 - 6.17: 5 6.17 - 7.71: 1 Bond angle restraints: 17647 Sorted by residual: angle pdb=" C ILE B 107 " pdb=" CA ILE B 107 " pdb=" CB ILE B 107 " ideal model delta sigma weight residual 112.14 106.33 5.81 1.35e+00 5.49e-01 1.85e+01 angle pdb=" C VAL A 66 " pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 111.94 107.84 4.10 1.26e+00 6.30e-01 1.06e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" C VAL A 66 " ideal model delta sigma weight residual 111.58 114.95 -3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" N GLN B 446 " pdb=" CA GLN B 446 " pdb=" C GLN B 446 " ideal model delta sigma weight residual 111.28 107.98 3.30 1.09e+00 8.42e-01 9.16e+00 angle pdb=" C VAL B 172 " pdb=" N PRO B 173 " pdb=" CA PRO B 173 " ideal model delta sigma weight residual 119.76 116.83 2.93 1.00e+00 1.00e+00 8.57e+00 ... (remaining 17642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6740 17.87 - 35.75: 585 35.75 - 53.62: 213 53.62 - 71.50: 43 71.50 - 89.37: 16 Dihedral angle restraints: 7597 sinusoidal: 2903 harmonic: 4694 Sorted by residual: dihedral pdb=" CA TYR A 115 " pdb=" C TYR A 115 " pdb=" N GLY A 116 " pdb=" CA GLY A 116 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASN D 33 " pdb=" C ASN D 33 " pdb=" N PHE D 34 " pdb=" CA PHE D 34 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN B 33 " pdb=" C ASN B 33 " pdb=" N PHE B 34 " pdb=" CA PHE B 34 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1450 0.030 - 0.060: 396 0.060 - 0.090: 153 0.090 - 0.121: 47 0.121 - 0.151: 6 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 2049 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 31 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" CG ASP A 31 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP A 31 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 31 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 172 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 173 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 130 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C ALA C 130 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA C 130 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS C 131 " -0.010 2.00e-02 2.50e+03 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 13234 3.28 - 3.82: 23583 3.82 - 4.36: 26220 4.36 - 4.90: 46609 Nonbonded interactions: 111059 Sorted by model distance: nonbonded pdb=" OE1 GLU D 70 " pdb=" N ASN D 72 " model vdw 2.199 3.120 nonbonded pdb=" N GLU A 178 " pdb=" OE1 GLU A 178 " model vdw 2.202 3.120 nonbonded pdb=" O PRO A 367 " pdb=" OG1 THR A 372 " model vdw 2.226 3.040 nonbonded pdb=" O ASP A 31 " pdb=" OD1 ASP A 31 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLN B 480 " pdb=" OH TYR C 474 " model vdw 2.236 3.040 ... (remaining 111054 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 0.032 13018 Z= 0.167 Angle : 0.510 7.707 17647 Z= 0.293 Chirality : 0.035 0.151 2052 Planarity : 0.003 0.042 2132 Dihedral : 16.232 89.371 4571 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 17.88 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.20), residues: 1578 helix: 2.78 (0.14), residues: 1235 sheet: 0.06 (0.70), residues: 48 loop : -0.53 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.012 0.001 TYR A 115 PHE 0.010 0.001 PHE B 34 TRP 0.006 0.001 TRP D 150 HIS 0.003 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (13018) covalent geometry : angle 0.51005 / 0.29 (17647) hydrogen bonds : bond 0.09719 / 6.53 ( 1066) hydrogen bonds : angle 4.64481 / 3.33 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 361 THR cc_start: 0.8765 (p) cc_final: 0.8377 (t) REVERT: A 386 MET cc_start: 0.6791 (mmm) cc_final: 0.6305 (tmt) REVERT: D 99 LYS cc_start: 0.8260 (pttp) cc_final: 0.7882 (pttt) outliers start: 0 outliers final: 1 residues processed: 194 average time/residue: 0.5758 time to fit residues: 121.7573 Evaluate side-chains 174 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN B 110 GLN B 125 HIS B 214 ASN C 214 ASN D 480 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.085595 restraints weight = 15040.483| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.54 r_work: 0.2697 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13018 Z= 0.131 Angle : 0.449 10.342 17647 Z= 0.242 Chirality : 0.036 0.135 2052 Planarity : 0.003 0.036 2132 Dihedral : 3.647 37.305 1712 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.09 % Allowed : 17.30 % Favored : 80.61 % 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: 3.88 (0.20), residues: 1578 helix: 3.23 (0.13), residues: 1242 sheet: 0.68 (0.77), residues: 42 loop : -0.30 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.012 0.001 TYR A 115 PHE 0.011 0.001 PHE D 194 TRP 0.010 0.001 TRP A 40 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13018) covalent geometry : angle 0.44871 / 0.24 (17647) hydrogen bonds : bond 0.05055 / 3.41 ( 1066) hydrogen bonds : angle 3.60705 / 2.56 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7368 (pt0) REVERT: A 167 MET cc_start: 0.8447 (mtm) cc_final: 0.8244 (mtm) REVERT: A 173 MET cc_start: 0.8233 (mtm) cc_final: 0.7955 (mtp) REVERT: A 239 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 386 MET cc_start: 0.6921 (mmm) cc_final: 0.6506 (tmt) REVERT: B 110 GLN cc_start: 0.8553 (pt0) cc_final: 0.8147 (mm-40) REVERT: C 229 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: C 389 THR cc_start: 0.8543 (m) cc_final: 0.8120 (p) REVERT: C 417 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8383 (p) REVERT: C 420 GLU cc_start: 0.8055 (tp30) cc_final: 0.7511 (mp0) REVERT: D 70 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: D 99 LYS cc_start: 0.8424 (pttp) cc_final: 0.8085 (pttt) REVERT: D 239 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8133 (tttm) REVERT: D 371 THR cc_start: 0.8872 (m) cc_final: 0.8630 (m) REVERT: D 466 SER cc_start: 0.8564 (m) cc_final: 0.8315 (p) outliers start: 29 outliers final: 10 residues processed: 216 average time/residue: 0.5875 time to fit residues: 137.9866 Evaluate side-chains 190 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.084563 restraints weight = 14939.205| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.48 r_work: 0.2723 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13018 Z= 0.223 Angle : 0.505 10.555 17647 Z= 0.269 Chirality : 0.039 0.138 2052 Planarity : 0.004 0.057 2132 Dihedral : 3.812 39.897 1712 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.45 % Allowed : 17.52 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.19), residues: 1578 helix: 3.09 (0.13), residues: 1236 sheet: -0.00 (0.71), residues: 48 loop : -0.38 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.015 0.001 TYR A 115 PHE 0.014 0.002 PHE D 194 TRP 0.008 0.001 TRP A 41 HIS 0.007 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (13018) covalent geometry : angle 0.50531 / 0.27 (17647) hydrogen bonds : bond 0.05692 / 3.83 ( 1066) hydrogen bonds : angle 3.74538 / 2.65 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 166 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 232 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 239 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 359 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7288 (p90) REVERT: A 386 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6756 (tmt) REVERT: B 110 GLN cc_start: 0.8592 (pt0) cc_final: 0.8269 (mm-40) REVERT: C 420 GLU cc_start: 0.8141 (tp30) cc_final: 0.7665 (mp0) REVERT: D 70 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: D 353 ASP cc_start: 0.8349 (m-30) cc_final: 0.8092 (m-30) REVERT: D 466 SER cc_start: 0.8721 (m) cc_final: 0.8440 (p) outliers start: 34 outliers final: 16 residues processed: 209 average time/residue: 0.4854 time to fit residues: 110.5085 Evaluate side-chains 194 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085027 restraints weight = 15132.922| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.54 r_work: 0.2690 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13018 Z= 0.123 Angle : 0.425 9.756 17647 Z= 0.230 Chirality : 0.036 0.134 2052 Planarity : 0.003 0.050 2132 Dihedral : 3.648 39.697 1712 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.45 % Allowed : 17.38 % Favored : 80.17 % 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: 3.96 (0.19), residues: 1578 helix: 3.29 (0.13), residues: 1242 sheet: 0.59 (0.75), residues: 42 loop : -0.30 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.012 0.001 TYR A 115 PHE 0.012 0.001 PHE A 171 TRP 0.010 0.001 TRP A 40 HIS 0.002 0.000 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13018) covalent geometry : angle 0.42482 / 0.23 (17647) hydrogen bonds : bond 0.04842 / 3.27 ( 1066) hydrogen bonds : angle 3.50734 / 2.49 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7334 (pt0) REVERT: A 208 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.6311 (t80) REVERT: A 232 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 239 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 359 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7217 (p90) REVERT: A 386 MET cc_start: 0.6701 (mmm) cc_final: 0.6444 (tmt) REVERT: B 99 LYS cc_start: 0.8357 (mtpm) cc_final: 0.7876 (ptmm) REVERT: B 110 GLN cc_start: 0.8514 (pt0) cc_final: 0.8074 (mm-40) REVERT: B 329 MET cc_start: 0.7635 (tpp) cc_final: 0.7429 (tpp) REVERT: C 229 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8742 (mm-30) REVERT: C 389 THR cc_start: 0.8470 (m) cc_final: 0.8110 (p) REVERT: C 420 GLU cc_start: 0.8013 (tp30) cc_final: 0.7378 (mp0) REVERT: D 339 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8502 (mm-30) REVERT: D 371 THR cc_start: 0.8839 (m) cc_final: 0.8580 (m) REVERT: D 466 SER cc_start: 0.8501 (m) cc_final: 0.8249 (p) outliers start: 34 outliers final: 11 residues processed: 208 average time/residue: 0.4976 time to fit residues: 112.8768 Evaluate side-chains 189 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.087228 restraints weight = 14929.509| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.49 r_work: 0.2790 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13018 Z= 0.146 Angle : 0.438 9.606 17647 Z= 0.237 Chirality : 0.036 0.134 2052 Planarity : 0.003 0.049 2132 Dihedral : 3.529 16.157 1710 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.16 % Allowed : 17.81 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.90 (0.19), residues: 1578 helix: 3.29 (0.13), residues: 1242 sheet: -0.07 (0.69), residues: 48 loop : -0.44 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.013 0.001 TYR A 115 PHE 0.013 0.001 PHE A 171 TRP 0.008 0.001 TRP A 40 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13018) covalent geometry : angle 0.43842 / 0.24 (17647) hydrogen bonds : bond 0.05026 / 3.39 ( 1066) hydrogen bonds : angle 3.54382 / 2.52 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7420 (pt0) REVERT: A 208 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.6487 (t80) REVERT: A 232 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 239 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 359 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7357 (p90) REVERT: B 99 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8088 (ptmm) REVERT: B 110 GLN cc_start: 0.8549 (pt0) cc_final: 0.8271 (mm-40) REVERT: C 229 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8840 (mm-30) REVERT: C 420 GLU cc_start: 0.8142 (tp30) cc_final: 0.7680 (mp0) REVERT: D 371 THR cc_start: 0.9018 (m) cc_final: 0.8759 (m) REVERT: D 466 SER cc_start: 0.8724 (m) cc_final: 0.8516 (p) outliers start: 30 outliers final: 14 residues processed: 203 average time/residue: 0.5438 time to fit residues: 120.0601 Evaluate side-chains 194 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 62 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.0000 chunk 83 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.086191 restraints weight = 15045.782| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.54 r_work: 0.2734 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13018 Z= 0.120 Angle : 0.410 9.672 17647 Z= 0.223 Chirality : 0.035 0.132 2052 Planarity : 0.003 0.049 2132 Dihedral : 3.451 15.272 1710 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.02 % Allowed : 17.66 % Favored : 80.32 % 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: 4.02 (0.20), residues: 1578 helix: 3.35 (0.13), residues: 1259 sheet: 0.44 (0.70), residues: 42 loop : -0.56 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.012 0.001 TYR A 115 PHE 0.011 0.001 PHE A 171 TRP 0.009 0.001 TRP A 40 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (13018) covalent geometry : angle 0.41026 / 0.22 (17647) hydrogen bonds : bond 0.04713 / 3.18 ( 1066) hydrogen bonds : angle 3.44587 / 2.45 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7206 (p) REVERT: A 124 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7361 (pt0) REVERT: A 208 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.6404 (t80) REVERT: A 239 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 359 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7289 (p90) REVERT: B 99 LYS cc_start: 0.8307 (mtpm) cc_final: 0.7916 (ptmm) REVERT: B 110 GLN cc_start: 0.8519 (pt0) cc_final: 0.8132 (mm-40) REVERT: B 248 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5236 (tp) REVERT: C 248 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4851 (mt) REVERT: C 389 THR cc_start: 0.8563 (m) cc_final: 0.8192 (p) REVERT: C 420 GLU cc_start: 0.8050 (tp30) cc_final: 0.7479 (mp0) REVERT: D 99 LYS cc_start: 0.8475 (pttp) cc_final: 0.8172 (pttt) REVERT: D 196 MET cc_start: 0.7895 (mmt) cc_final: 0.7400 (mtt) REVERT: D 339 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8558 (mm-30) REVERT: D 371 THR cc_start: 0.8887 (m) cc_final: 0.8612 (m) REVERT: D 466 SER cc_start: 0.8537 (m) cc_final: 0.8336 (p) outliers start: 28 outliers final: 11 residues processed: 201 average time/residue: 0.4914 time to fit residues: 107.9566 Evaluate side-chains 187 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.084058 restraints weight = 15182.391| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.56 r_work: 0.2707 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13018 Z= 0.141 Angle : 0.432 10.109 17647 Z= 0.233 Chirality : 0.036 0.145 2052 Planarity : 0.003 0.049 2132 Dihedral : 3.490 15.266 1710 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.87 % Allowed : 17.95 % Favored : 80.17 % 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: 3.95 (0.19), residues: 1578 helix: 3.34 (0.13), residues: 1247 sheet: -0.28 (0.66), residues: 48 loop : -0.49 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.013 0.001 TYR A 115 PHE 0.012 0.001 PHE B 220 TRP 0.008 0.001 TRP A 40 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13018) covalent geometry : angle 0.43231 / 0.23 (17647) hydrogen bonds : bond 0.04914 / 3.32 ( 1066) hydrogen bonds : angle 3.49774 / 2.49 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7383 (pt0) REVERT: A 208 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.6333 (t80) REVERT: A 232 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 239 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 359 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 99 LYS cc_start: 0.8451 (mtpm) cc_final: 0.8001 (ptmm) REVERT: B 110 GLN cc_start: 0.8567 (pt0) cc_final: 0.8142 (mm-40) REVERT: B 119 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: C 248 LEU cc_start: 0.5154 (OUTLIER) cc_final: 0.4906 (mt) REVERT: C 389 THR cc_start: 0.8575 (m) cc_final: 0.8141 (p) REVERT: C 417 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8356 (p) REVERT: C 420 GLU cc_start: 0.8042 (tp30) cc_final: 0.7498 (mp0) REVERT: D 99 LYS cc_start: 0.8505 (pttp) cc_final: 0.8178 (pttt) REVERT: D 141 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 196 MET cc_start: 0.7901 (mmt) cc_final: 0.7403 (mtt) REVERT: D 339 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8596 (mm-30) REVERT: D 466 SER cc_start: 0.8545 (m) cc_final: 0.8332 (p) outliers start: 26 outliers final: 13 residues processed: 202 average time/residue: 0.5242 time to fit residues: 115.4765 Evaluate side-chains 192 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085049 restraints weight = 15058.445| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.54 r_work: 0.2712 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13018 Z= 0.127 Angle : 0.425 10.706 17647 Z= 0.229 Chirality : 0.036 0.174 2052 Planarity : 0.003 0.049 2132 Dihedral : 3.466 15.266 1710 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.66 % Allowed : 18.17 % Favored : 80.17 % 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: 3.98 (0.19), residues: 1578 helix: 3.34 (0.13), residues: 1259 sheet: 0.18 (0.68), residues: 42 loop : -0.63 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.012 0.001 TYR A 115 PHE 0.013 0.001 PHE A 171 TRP 0.008 0.001 TRP A 41 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13018) covalent geometry : angle 0.42463 / 0.23 (17647) hydrogen bonds : bond 0.04766 / 3.22 ( 1066) hydrogen bonds : angle 3.45502 / 2.46 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7365 (pt0) REVERT: A 208 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 232 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 239 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 359 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7235 (p90) REVERT: B 110 GLN cc_start: 0.8550 (pt0) cc_final: 0.8131 (mm-40) REVERT: B 119 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: C 248 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4932 (mt) REVERT: C 389 THR cc_start: 0.8579 (m) cc_final: 0.8173 (p) REVERT: C 417 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 420 GLU cc_start: 0.8046 (tp30) cc_final: 0.7669 (tm-30) REVERT: D 99 LYS cc_start: 0.8496 (pttp) cc_final: 0.8169 (pttt) REVERT: D 196 MET cc_start: 0.7900 (mmt) cc_final: 0.7401 (mtt) REVERT: D 371 THR cc_start: 0.8880 (m) cc_final: 0.8569 (m) REVERT: D 466 SER cc_start: 0.8515 (m) cc_final: 0.8311 (p) outliers start: 23 outliers final: 11 residues processed: 197 average time/residue: 0.4946 time to fit residues: 106.1930 Evaluate side-chains 191 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.082670 restraints weight = 15276.430| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.55 r_work: 0.2671 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13018 Z= 0.168 Angle : 0.459 10.752 17647 Z= 0.245 Chirality : 0.037 0.134 2052 Planarity : 0.003 0.050 2132 Dihedral : 3.548 15.275 1710 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.80 % Allowed : 18.24 % Favored : 79.96 % 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 are not related in a simple way. whole: 3.86 (0.19), residues: 1578 helix: 3.29 (0.13), residues: 1239 sheet: -0.44 (0.66), residues: 48 loop : -0.45 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.014 0.001 TYR A 115 PHE 0.012 0.001 PHE B 84 TRP 0.006 0.001 TRP A 41 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13018) covalent geometry : angle 0.45864 / 0.25 (17647) hydrogen bonds : bond 0.05158 / 3.48 ( 1066) hydrogen bonds : angle 3.56946 / 2.54 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7411 (pt0) REVERT: A 208 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 232 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 239 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 359 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7323 (p90) REVERT: B 110 GLN cc_start: 0.8596 (pt0) cc_final: 0.8147 (mm-40) REVERT: B 119 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: C 248 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4936 (mt) REVERT: C 417 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8346 (p) REVERT: C 420 GLU cc_start: 0.8032 (tp30) cc_final: 0.7494 (mp0) REVERT: D 99 LYS cc_start: 0.8505 (pttp) cc_final: 0.8178 (pttt) REVERT: D 196 MET cc_start: 0.7910 (mmt) cc_final: 0.7400 (mtt) REVERT: D 466 SER cc_start: 0.8578 (m) cc_final: 0.8328 (p) outliers start: 25 outliers final: 16 residues processed: 190 average time/residue: 0.5311 time to fit residues: 109.9872 Evaluate side-chains 193 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 478 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.085746 restraints weight = 15185.054| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.55 r_work: 0.2689 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13018 Z= 0.125 Angle : 0.424 10.365 17647 Z= 0.228 Chirality : 0.035 0.132 2052 Planarity : 0.003 0.051 2132 Dihedral : 3.471 15.145 1710 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.20), residues: 1578 helix: 3.32 (0.13), residues: 1259 sheet: -0.45 (0.66), residues: 48 loop : -0.72 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.012 0.001 TYR A 115 PHE 0.012 0.001 PHE B 220 TRP 0.008 0.001 TRP A 40 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13018) covalent geometry : angle 0.42398 / 0.23 (17647) hydrogen bonds : bond 0.04749 / 3.21 ( 1066) hydrogen bonds : angle 3.46159 / 2.47 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7319 (pt0) REVERT: A 208 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6371 (t80) REVERT: A 232 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 239 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 359 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7282 (p90) REVERT: B 110 GLN cc_start: 0.8531 (pt0) cc_final: 0.8067 (mm-40) REVERT: B 119 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 248 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4846 (mt) REVERT: C 389 THR cc_start: 0.8493 (m) cc_final: 0.8066 (p) REVERT: C 417 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 420 GLU cc_start: 0.7987 (tp30) cc_final: 0.7554 (tm-30) REVERT: D 99 LYS cc_start: 0.8437 (pttp) cc_final: 0.8110 (pttt) REVERT: D 196 MET cc_start: 0.7840 (mmt) cc_final: 0.7315 (mtt) REVERT: D 339 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8446 (mm-30) REVERT: D 371 THR cc_start: 0.8815 (m) cc_final: 0.8535 (m) REVERT: D 466 SER cc_start: 0.8437 (m) cc_final: 0.8208 (p) outliers start: 21 outliers final: 12 residues processed: 188 average time/residue: 0.6090 time to fit residues: 124.9924 Evaluate side-chains 186 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS B 446 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.083754 restraints weight = 15191.002| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.56 r_work: 0.2680 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13018 Z= 0.146 Angle : 0.443 10.536 17647 Z= 0.237 Chirality : 0.036 0.135 2052 Planarity : 0.003 0.050 2132 Dihedral : 3.501 15.241 1710 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.59 % Allowed : 18.89 % Favored : 79.52 % 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: 3.89 (0.19), residues: 1578 helix: 3.31 (0.13), residues: 1247 sheet: -0.46 (0.65), residues: 48 loop : -0.54 (0.32), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.013 0.001 TYR A 115 PHE 0.012 0.001 PHE B 220 TRP 0.007 0.001 TRP A 41 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13018) covalent geometry : angle 0.44302 / 0.24 (17647) hydrogen bonds : bond 0.04945 / 3.34 ( 1066) hydrogen bonds : angle 3.50938 / 2.50 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.69 seconds wall clock time: 63 minutes 52.77 seconds (3832.77 seconds total)