Starting phenix.real_space_refine on Fri Aug 22 16:20:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.map" model { file = "/net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gb3_29912/08_2025/8gb3_29912.cif" } resolution = 3.7 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 242 atoms to isotropic. 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 8 5.16 5 C 3420 2.51 5 N 996 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5537 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3814 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1051 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 672 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 1.47, per 1000 atoms: 0.27 Number of scatterers: 5537 At special positions: 0 Unit cell: (68.724, 86.112, 106.812, 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 8 16.00 O 1113 8.00 N 996 7.00 C 3420 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: 0.36 Conformation dependent library (CDL) restraints added in 169.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 46.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'D' and resid 51 through 61 removed outlier: 4.390A pdb=" N GLN D 57 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 4.289A pdb=" N SER D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 200 through 220 removed outlier: 3.640A pdb=" N TRP D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 274 through 288 removed outlier: 6.054A pdb=" N ASP D 284 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 300 removed outlier: 4.251A pdb=" N THR D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.521A pdb=" N THR D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.508A pdb=" N LYS D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 496 removed outlier: 3.736A pdb=" N ASP D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 488 " --> pdb=" O GLU D 484 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 491 " --> pdb=" O ASP D 487 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 removed outlier: 3.760A pdb=" N GLU D 505 " --> pdb=" O ARG D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'E' and resid 45 through 79 removed outlier: 3.592A pdb=" N GLN E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.866A pdb=" N ALA E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.950A pdb=" N GLY E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 83 removed outlier: 3.773A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.677A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 107 removed outlier: 4.117A pdb=" N GLY F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 117 through 130 removed outlier: 4.119A pdb=" N ASP F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.769A pdb=" N VAL D 16 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA D 4 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 177 through 181 Processing sheet with id=AA3, first strand: chain 'D' and resid 381 through 386 removed outlier: 3.747A pdb=" N LEU D 385 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU D 373 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN D 413 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY D 429 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN D 416 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU D 427 " --> pdb=" O GLN D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 169 removed outlier: 3.577A pdb=" N VAL E 163 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY E 185 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL E 167 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU E 183 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 172 through 174 removed outlier: 7.796A pdb=" N TYR E 172 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 179 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 174 " --> pdb=" O GLN E 177 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 768 1.46 - 1.57: 2847 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 5597 Sorted by residual: bond pdb=" CA ILE D 39 " pdb=" CB ILE D 39 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.39e+00 bond pdb=" CG PRO D 393 " pdb=" CD PRO D 393 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.47e-01 bond pdb=" CB PRO D 148 " pdb=" CG PRO D 148 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 6.93e-01 bond pdb=" CB VAL D 345 " pdb=" CG1 VAL D 345 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.44e-01 bond pdb=" C LYS D 361 " pdb=" O LYS D 361 " ideal model delta sigma weight residual 1.242 1.234 0.008 1.00e-02 1.00e+04 6.26e-01 ... (remaining 5592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 7272 1.17 - 2.34: 240 2.34 - 3.51: 43 3.51 - 4.68: 10 4.68 - 5.85: 4 Bond angle restraints: 7569 Sorted by residual: angle pdb=" C LYS D 361 " pdb=" CA LYS D 361 " pdb=" CB LYS D 361 " ideal model delta sigma weight residual 116.63 110.78 5.85 1.16e+00 7.43e-01 2.54e+01 angle pdb=" C THR D 391 " pdb=" N ILE D 392 " pdb=" CA ILE D 392 " ideal model delta sigma weight residual 120.43 124.79 -4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" C ILE D 144 " pdb=" N VAL D 145 " pdb=" CA VAL D 145 " ideal model delta sigma weight residual 120.49 125.08 -4.59 1.38e+00 5.25e-01 1.10e+01 angle pdb=" CA LYS D 361 " pdb=" C LYS D 361 " pdb=" N ASP D 362 " ideal model delta sigma weight residual 119.63 117.09 2.54 8.10e-01 1.52e+00 9.84e+00 angle pdb=" C ILE D 392 " pdb=" CA ILE D 392 " pdb=" CB ILE D 392 " ideal model delta sigma weight residual 113.70 110.84 2.86 9.50e-01 1.11e+00 9.03e+00 ... (remaining 7564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 3139 15.77 - 31.55: 214 31.55 - 47.32: 59 47.32 - 63.10: 14 63.10 - 78.87: 6 Dihedral angle restraints: 3432 sinusoidal: 1348 harmonic: 2084 Sorted by residual: dihedral pdb=" CA ALA D 105 " pdb=" C ALA D 105 " pdb=" N TYR D 106 " pdb=" CA TYR D 106 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU D 366 " pdb=" C LEU D 366 " pdb=" N ASP D 367 " pdb=" CA ASP D 367 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN D 45 " pdb=" C ASN D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.051: 219 0.051 - 0.076: 96 0.076 - 0.102: 43 0.102 - 0.127: 33 Chirality restraints: 889 Sorted by residual: chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE D 253 " pdb=" N ILE D 253 " pdb=" C ILE D 253 " pdb=" CB ILE D 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CB ILE D 443 " pdb=" CA ILE D 443 " pdb=" CG1 ILE D 443 " pdb=" CG2 ILE D 443 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 886 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 291 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO D 292 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 292 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 292 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 118 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO D 119 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 52 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO D 53 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 53 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 53 " 0.018 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1115 2.78 - 3.31: 5743 3.31 - 3.84: 9218 3.84 - 4.37: 10395 4.37 - 4.90: 17457 Nonbonded interactions: 43928 Sorted by model distance: nonbonded pdb=" O ILE D 307 " pdb=" NZ LYS D 333 " model vdw 2.245 3.120 nonbonded pdb=" O PHE D 278 " pdb=" OG1 THR D 282 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP D 464 " pdb=" OG1 THR D 467 " model vdw 2.249 3.040 nonbonded pdb=" O PRO E 115 " pdb=" OG SER E 118 " model vdw 2.268 3.040 nonbonded pdb=" N GLU E 148 " pdb=" O ALA E 182 " model vdw 2.299 3.120 ... (remaining 43923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.290 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.060 Find NCS groups from input model: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 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 0.042 5597 Z= 0.138 Angle : 0.522 5.846 7569 Z= 0.305 Chirality : 0.041 0.127 889 Planarity : 0.004 0.038 1008 Dihedral : 12.387 78.869 2086 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.31 % Allowed : 8.97 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.33), residues: 723 helix: 1.00 (0.31), residues: 309 sheet: -0.68 (0.55), residues: 101 loop : -1.39 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 104 TYR 0.006 0.001 TYR D 106 PHE 0.011 0.001 PHE D 176 TRP 0.007 0.001 TRP D 211 HIS 0.001 0.000 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5597) covalent geometry : angle 0.52179 ( 7569) hydrogen bonds : bond 0.17009 ( 261) hydrogen bonds : angle 6.11906 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6699 (m-40) cc_final: 0.6446 (m-40) REVERT: D 100 LYS cc_start: 0.7758 (tttm) cc_final: 0.7533 (tttm) REVERT: D 166 ILE cc_start: 0.7430 (tp) cc_final: 0.7220 (tp) REVERT: D 227 ASP cc_start: 0.6805 (m-30) cc_final: 0.6598 (m-30) REVERT: D 229 MET cc_start: 0.5748 (tpt) cc_final: 0.5399 (tpt) REVERT: D 283 GLN cc_start: 0.6353 (tp-100) cc_final: 0.5803 (tp-100) REVERT: D 333 LYS cc_start: 0.7242 (ttmt) cc_final: 0.6792 (ttmt) REVERT: D 356 LEU cc_start: 0.7988 (mm) cc_final: 0.7552 (mm) REVERT: D 357 LYS cc_start: 0.8056 (pttm) cc_final: 0.7728 (pttm) REVERT: D 359 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6442 (mm-30) REVERT: D 383 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7867 (p) REVERT: D 395 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7304 (tmtt) REVERT: D 416 GLN cc_start: 0.7787 (pm20) cc_final: 0.7439 (pm20) REVERT: D 489 MET cc_start: 0.6065 (mpp) cc_final: 0.5466 (mpp) REVERT: E 63 GLN cc_start: 0.6875 (pm20) cc_final: 0.6522 (pm20) REVERT: F 69 PHE cc_start: 0.7108 (t80) cc_final: 0.6471 (t80) REVERT: F 117 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7079 (ttmm) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.0876 time to fit residues: 14.6208 Evaluate side-chains 116 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 425 ASN E 80 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** 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 = 0.4520 r_free = 0.4520 target = 0.195489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.164996 restraints weight = 8980.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.169979 restraints weight = 5324.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.173421 restraints weight = 3514.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.176091 restraints weight = 2509.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.177610 restraints weight = 1911.379| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5597 Z= 0.165 Angle : 0.609 10.595 7569 Z= 0.317 Chirality : 0.044 0.186 889 Planarity : 0.004 0.040 1008 Dihedral : 7.483 59.149 809 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.66 % Allowed : 11.90 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.32), residues: 723 helix: 0.80 (0.29), residues: 321 sheet: -0.77 (0.54), residues: 105 loop : -1.54 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.008 0.001 TYR D 155 PHE 0.015 0.002 PHE D 122 TRP 0.010 0.002 TRP D 204 HIS 0.006 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5597) covalent geometry : angle 0.60943 ( 7569) hydrogen bonds : bond 0.04443 ( 261) hydrogen bonds : angle 4.85070 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6608 (m-40) cc_final: 0.6288 (m-40) REVERT: D 100 LYS cc_start: 0.7797 (tttm) cc_final: 0.7592 (tttm) REVERT: D 166 ILE cc_start: 0.7301 (tp) cc_final: 0.7058 (tp) REVERT: D 182 GLU cc_start: 0.4445 (mt-10) cc_final: 0.4037 (mt-10) REVERT: D 229 MET cc_start: 0.5731 (tpt) cc_final: 0.5387 (tpt) REVERT: D 239 GLU cc_start: 0.7228 (tp30) cc_final: 0.6739 (tp30) REVERT: D 249 GLN cc_start: 0.7613 (pp30) cc_final: 0.7360 (pp30) REVERT: D 283 GLN cc_start: 0.6229 (tp-100) cc_final: 0.5736 (tp-100) REVERT: D 297 ILE cc_start: 0.2591 (OUTLIER) cc_final: 0.2214 (tt) REVERT: D 356 LEU cc_start: 0.8013 (mm) cc_final: 0.7557 (mm) REVERT: D 357 LYS cc_start: 0.7968 (pttm) cc_final: 0.7740 (pttm) REVERT: D 359 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6412 (mm-30) REVERT: D 395 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7347 (tmtt) REVERT: D 416 GLN cc_start: 0.7803 (pm20) cc_final: 0.7460 (pm20) REVERT: E 63 GLN cc_start: 0.6820 (pm20) cc_final: 0.6525 (pm20) REVERT: F 69 PHE cc_start: 0.7231 (t80) cc_final: 0.6486 (t80) REVERT: F 75 ARG cc_start: 0.7037 (ttp-110) cc_final: 0.6726 (ttp-110) REVERT: F 78 ARG cc_start: 0.6848 (mmm160) cc_final: 0.6313 (mmm160) REVERT: F 117 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7135 (ttmm) outliers start: 27 outliers final: 13 residues processed: 123 average time/residue: 0.0921 time to fit residues: 13.8995 Evaluate side-chains 121 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.197147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.167112 restraints weight = 8858.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.172115 restraints weight = 5237.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.175503 restraints weight = 3437.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.178281 restraints weight = 2453.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179814 restraints weight = 1843.416| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5597 Z= 0.129 Angle : 0.583 12.249 7569 Z= 0.300 Chirality : 0.043 0.132 889 Planarity : 0.004 0.036 1008 Dihedral : 6.667 59.873 802 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.83 % Allowed : 13.79 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.32), residues: 723 helix: 1.22 (0.30), residues: 309 sheet: -0.65 (0.59), residues: 87 loop : -1.55 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 180 TYR 0.005 0.001 TYR D 155 PHE 0.014 0.001 PHE D 122 TRP 0.009 0.001 TRP D 204 HIS 0.006 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5597) covalent geometry : angle 0.58314 ( 7569) hydrogen bonds : bond 0.03856 ( 261) hydrogen bonds : angle 4.56117 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6549 (m-40) cc_final: 0.6194 (m-40) REVERT: D 100 LYS cc_start: 0.7808 (tttm) cc_final: 0.7594 (tttm) REVERT: D 166 ILE cc_start: 0.7319 (tp) cc_final: 0.7077 (tp) REVERT: D 182 GLU cc_start: 0.4429 (mt-10) cc_final: 0.4101 (mt-10) REVERT: D 229 MET cc_start: 0.5672 (tpt) cc_final: 0.5349 (tpt) REVERT: D 249 GLN cc_start: 0.7585 (pp30) cc_final: 0.7298 (pp30) REVERT: D 283 GLN cc_start: 0.6267 (tp-100) cc_final: 0.5729 (tp-100) REVERT: D 297 ILE cc_start: 0.2499 (OUTLIER) cc_final: 0.2114 (tt) REVERT: D 356 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7556 (mm) REVERT: D 357 LYS cc_start: 0.8036 (pttm) cc_final: 0.7758 (pttm) REVERT: D 359 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6425 (mm-30) REVERT: D 395 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7250 (tmtt) REVERT: D 396 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6618 (tpt-90) REVERT: D 416 GLN cc_start: 0.7805 (pm20) cc_final: 0.7578 (pm20) REVERT: E 63 GLN cc_start: 0.6859 (pm20) cc_final: 0.6570 (pm20) REVERT: F 64 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6785 (mmm-85) REVERT: F 69 PHE cc_start: 0.7145 (t80) cc_final: 0.6469 (t80) REVERT: F 102 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5757 (pp) REVERT: F 117 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7196 (tppp) outliers start: 28 outliers final: 15 residues processed: 124 average time/residue: 0.0918 time to fit residues: 13.7835 Evaluate side-chains 124 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 24 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.196465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165846 restraints weight = 8904.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170939 restraints weight = 5269.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.174733 restraints weight = 3445.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.177059 restraints weight = 2419.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179049 restraints weight = 1847.798| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5597 Z= 0.143 Angle : 0.578 11.980 7569 Z= 0.301 Chirality : 0.043 0.136 889 Planarity : 0.004 0.036 1008 Dihedral : 6.712 59.835 802 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.83 % Allowed : 14.48 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.32), residues: 723 helix: 1.27 (0.30), residues: 309 sheet: -0.60 (0.57), residues: 92 loop : -1.61 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 75 TYR 0.009 0.001 TYR D 155 PHE 0.015 0.001 PHE D 122 TRP 0.009 0.001 TRP D 204 HIS 0.006 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5597) covalent geometry : angle 0.57783 ( 7569) hydrogen bonds : bond 0.03658 ( 261) hydrogen bonds : angle 4.48083 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6516 (m-40) cc_final: 0.6174 (m-40) REVERT: D 100 LYS cc_start: 0.7795 (tttm) cc_final: 0.7574 (tttm) REVERT: D 107 LEU cc_start: 0.7395 (mp) cc_final: 0.6416 (mt) REVERT: D 166 ILE cc_start: 0.7330 (tp) cc_final: 0.7097 (tp) REVERT: D 182 GLU cc_start: 0.4432 (mt-10) cc_final: 0.4017 (mt-10) REVERT: D 229 MET cc_start: 0.5614 (tpt) cc_final: 0.5351 (tpt) REVERT: D 272 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: D 283 GLN cc_start: 0.6164 (tp-100) cc_final: 0.5713 (tp-100) REVERT: D 297 ILE cc_start: 0.2542 (OUTLIER) cc_final: 0.2192 (tt) REVERT: D 356 LEU cc_start: 0.8000 (mm) cc_final: 0.7543 (mm) REVERT: D 357 LYS cc_start: 0.8087 (pttm) cc_final: 0.7820 (pttm) REVERT: D 359 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6419 (mm-30) REVERT: D 395 LYS cc_start: 0.7745 (tmtt) cc_final: 0.7359 (tmtt) REVERT: D 396 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6641 (tpt-90) REVERT: E 63 GLN cc_start: 0.6869 (pm20) cc_final: 0.6527 (pm20) REVERT: F 69 PHE cc_start: 0.7176 (t80) cc_final: 0.6456 (t80) REVERT: F 102 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5718 (pp) REVERT: F 117 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7325 (tppp) outliers start: 28 outliers final: 19 residues processed: 124 average time/residue: 0.0925 time to fit residues: 13.9739 Evaluate side-chains 129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 21 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.196580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.166237 restraints weight = 9059.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171257 restraints weight = 5362.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.175039 restraints weight = 3496.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177312 restraints weight = 2462.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.179241 restraints weight = 1880.145| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5597 Z= 0.175 Angle : 0.602 10.937 7569 Z= 0.313 Chirality : 0.044 0.167 889 Planarity : 0.004 0.036 1008 Dihedral : 6.857 59.804 802 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.69 % Allowed : 14.83 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.32), residues: 723 helix: 1.23 (0.30), residues: 309 sheet: -0.65 (0.57), residues: 92 loop : -1.62 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 75 TYR 0.011 0.001 TYR D 155 PHE 0.013 0.001 PHE D 122 TRP 0.008 0.001 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5597) covalent geometry : angle 0.60169 ( 7569) hydrogen bonds : bond 0.03840 ( 261) hydrogen bonds : angle 4.58197 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6523 (m-40) cc_final: 0.6171 (m-40) REVERT: D 90 GLU cc_start: 0.7724 (mp0) cc_final: 0.7184 (mp0) REVERT: D 100 LYS cc_start: 0.7783 (tttm) cc_final: 0.7540 (tttm) REVERT: D 166 ILE cc_start: 0.7419 (tp) cc_final: 0.7191 (tp) REVERT: D 182 GLU cc_start: 0.4599 (mt-10) cc_final: 0.4236 (mt-10) REVERT: D 215 LYS cc_start: 0.6750 (tptp) cc_final: 0.6453 (tptp) REVERT: D 229 MET cc_start: 0.5705 (tpt) cc_final: 0.5419 (tpt) REVERT: D 249 GLN cc_start: 0.7604 (pp30) cc_final: 0.7360 (pp30) REVERT: D 272 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: D 283 GLN cc_start: 0.6153 (tp-100) cc_final: 0.5735 (tp-100) REVERT: D 297 ILE cc_start: 0.2762 (OUTLIER) cc_final: 0.2377 (tt) REVERT: D 356 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7628 (mm) REVERT: D 359 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6396 (mm-30) REVERT: D 395 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7198 (tmtt) REVERT: D 396 ARG cc_start: 0.6967 (tpt170) cc_final: 0.6673 (tpt-90) REVERT: E 63 GLN cc_start: 0.6809 (pm20) cc_final: 0.6484 (pm20) REVERT: F 64 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6816 (mmm-85) REVERT: F 69 PHE cc_start: 0.7172 (t80) cc_final: 0.6327 (t80) REVERT: F 102 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5655 (pp) REVERT: F 117 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7334 (tppp) REVERT: F 122 LYS cc_start: 0.7957 (tptt) cc_final: 0.7604 (tptt) outliers start: 33 outliers final: 21 residues processed: 129 average time/residue: 0.0857 time to fit residues: 13.6325 Evaluate side-chains 135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.196270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.166210 restraints weight = 8938.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.171148 restraints weight = 5340.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.174376 restraints weight = 3531.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.177103 restraints weight = 2547.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.178764 restraints weight = 1926.499| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5597 Z= 0.145 Angle : 0.594 11.237 7569 Z= 0.309 Chirality : 0.043 0.138 889 Planarity : 0.004 0.035 1008 Dihedral : 6.818 59.522 802 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.34 % Allowed : 16.21 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.32), residues: 723 helix: 1.29 (0.30), residues: 309 sheet: -0.49 (0.58), residues: 89 loop : -1.66 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 75 TYR 0.008 0.001 TYR D 155 PHE 0.014 0.001 PHE D 122 TRP 0.009 0.001 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5597) covalent geometry : angle 0.59424 ( 7569) hydrogen bonds : bond 0.03637 ( 261) hydrogen bonds : angle 4.50010 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7675 (mp0) cc_final: 0.7174 (mp0) REVERT: D 100 LYS cc_start: 0.7824 (tttm) cc_final: 0.7584 (tttm) REVERT: D 166 ILE cc_start: 0.7322 (tp) cc_final: 0.7120 (tp) REVERT: D 182 GLU cc_start: 0.4411 (mt-10) cc_final: 0.4072 (mm-30) REVERT: D 215 LYS cc_start: 0.6718 (tptp) cc_final: 0.6449 (tptp) REVERT: D 229 MET cc_start: 0.5657 (tpt) cc_final: 0.5412 (tpt) REVERT: D 249 GLN cc_start: 0.7588 (pp30) cc_final: 0.7344 (pp30) REVERT: D 272 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6433 (pm20) REVERT: D 283 GLN cc_start: 0.6114 (tp-100) cc_final: 0.5722 (tp-100) REVERT: D 297 ILE cc_start: 0.2782 (OUTLIER) cc_final: 0.2411 (tt) REVERT: D 356 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7632 (mm) REVERT: D 359 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6430 (mm-30) REVERT: D 395 LYS cc_start: 0.7702 (tmtt) cc_final: 0.7140 (tmtt) REVERT: D 396 ARG cc_start: 0.6835 (tpt170) cc_final: 0.6532 (tpt-90) REVERT: E 63 GLN cc_start: 0.6810 (pm20) cc_final: 0.6512 (pm20) REVERT: F 64 ARG cc_start: 0.7007 (mmm-85) cc_final: 0.6783 (mmm-85) REVERT: F 69 PHE cc_start: 0.7241 (t80) cc_final: 0.6403 (t80) REVERT: F 102 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5735 (pp) REVERT: F 117 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7318 (tppp) REVERT: F 122 LYS cc_start: 0.7888 (tptt) cc_final: 0.7575 (tptt) outliers start: 31 outliers final: 20 residues processed: 127 average time/residue: 0.0774 time to fit residues: 11.9734 Evaluate side-chains 132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 70 optimal weight: 0.0970 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.196086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.165720 restraints weight = 8962.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.170679 restraints weight = 5399.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174227 restraints weight = 3549.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.176482 restraints weight = 2534.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.178342 restraints weight = 1946.926| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5597 Z= 0.159 Angle : 0.598 11.346 7569 Z= 0.310 Chirality : 0.043 0.139 889 Planarity : 0.004 0.035 1008 Dihedral : 6.844 59.235 802 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.21 % Allowed : 15.00 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.32), residues: 723 helix: 1.28 (0.30), residues: 309 sheet: -0.51 (0.58), residues: 89 loop : -1.69 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 75 TYR 0.008 0.001 TYR D 155 PHE 0.014 0.001 PHE D 122 TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5597) covalent geometry : angle 0.59779 ( 7569) hydrogen bonds : bond 0.03697 ( 261) hydrogen bonds : angle 4.48851 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7665 (mp0) cc_final: 0.7341 (mp0) REVERT: D 100 LYS cc_start: 0.7820 (tttm) cc_final: 0.7578 (tttm) REVERT: D 166 ILE cc_start: 0.7342 (tp) cc_final: 0.7135 (tp) REVERT: D 182 GLU cc_start: 0.4412 (mt-10) cc_final: 0.3911 (mm-30) REVERT: D 215 LYS cc_start: 0.6725 (tptp) cc_final: 0.6442 (tptp) REVERT: D 229 MET cc_start: 0.5602 (tpt) cc_final: 0.5203 (tpt) REVERT: D 231 MET cc_start: 0.5262 (mmt) cc_final: 0.4682 (mmt) REVERT: D 249 GLN cc_start: 0.7607 (pp30) cc_final: 0.7350 (pp30) REVERT: D 272 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: D 283 GLN cc_start: 0.6158 (tp-100) cc_final: 0.5718 (tp-100) REVERT: D 297 ILE cc_start: 0.2837 (OUTLIER) cc_final: 0.2463 (tt) REVERT: D 356 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7608 (mm) REVERT: D 359 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6547 (mm-30) REVERT: D 395 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7313 (tmtt) REVERT: D 396 ARG cc_start: 0.6880 (tpt170) cc_final: 0.6553 (tpt-90) REVERT: E 63 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6547 (pm20) REVERT: F 69 PHE cc_start: 0.7263 (t80) cc_final: 0.6421 (t80) REVERT: F 102 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5648 (pp) REVERT: F 117 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7384 (tppp) REVERT: F 122 LYS cc_start: 0.7879 (tptt) cc_final: 0.7567 (tptt) outliers start: 36 outliers final: 19 residues processed: 127 average time/residue: 0.0902 time to fit residues: 13.8061 Evaluate side-chains 133 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.197985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.168201 restraints weight = 8777.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.173130 restraints weight = 5291.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.176651 restraints weight = 3485.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.178980 restraints weight = 2480.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.180905 restraints weight = 1888.853| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5597 Z= 0.134 Angle : 0.600 11.411 7569 Z= 0.308 Chirality : 0.043 0.141 889 Planarity : 0.004 0.035 1008 Dihedral : 6.786 59.101 802 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.86 % Allowed : 15.34 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.32), residues: 723 helix: 1.36 (0.30), residues: 312 sheet: -0.56 (0.58), residues: 84 loop : -1.77 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 180 TYR 0.006 0.001 TYR D 155 PHE 0.013 0.001 PHE D 122 TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5597) covalent geometry : angle 0.60026 ( 7569) hydrogen bonds : bond 0.03467 ( 261) hydrogen bonds : angle 4.37007 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7639 (mp0) cc_final: 0.7338 (mp0) REVERT: D 100 LYS cc_start: 0.7827 (tttm) cc_final: 0.7572 (tttm) REVERT: D 215 LYS cc_start: 0.6708 (tptp) cc_final: 0.6463 (tptm) REVERT: D 229 MET cc_start: 0.5595 (tpt) cc_final: 0.5325 (tpt) REVERT: D 249 GLN cc_start: 0.7575 (pp30) cc_final: 0.7322 (pp30) REVERT: D 272 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: D 283 GLN cc_start: 0.6078 (tp-100) cc_final: 0.5725 (tp-100) REVERT: D 297 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2440 (tt) REVERT: D 356 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7583 (mm) REVERT: D 359 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6569 (mm-30) REVERT: D 395 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7306 (tmtt) REVERT: D 396 ARG cc_start: 0.6882 (tpt170) cc_final: 0.6580 (tpt-90) REVERT: D 416 GLN cc_start: 0.8528 (pp30) cc_final: 0.8313 (pm20) REVERT: E 63 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6555 (pm20) REVERT: F 69 PHE cc_start: 0.7275 (t80) cc_final: 0.6450 (t80) REVERT: F 102 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5663 (pp) REVERT: F 117 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7401 (tppp) REVERT: F 122 LYS cc_start: 0.7838 (tptt) cc_final: 0.7545 (tptt) outliers start: 34 outliers final: 22 residues processed: 128 average time/residue: 0.0869 time to fit residues: 13.6041 Evaluate side-chains 132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN F 66 GLN ** F 80 GLN ** 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 = 0.4540 r_free = 0.4540 target = 0.197760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.167395 restraints weight = 8859.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.172272 restraints weight = 5332.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.175959 restraints weight = 3514.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178170 restraints weight = 2496.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.180055 restraints weight = 1917.474| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5597 Z= 0.143 Angle : 0.621 11.197 7569 Z= 0.319 Chirality : 0.045 0.227 889 Planarity : 0.004 0.056 1008 Dihedral : 6.846 59.963 802 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.52 % Allowed : 16.55 % Favored : 77.93 % 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 aren not related in a simple way. whole: -0.31 (0.32), residues: 723 helix: 1.39 (0.30), residues: 312 sheet: -0.52 (0.58), residues: 84 loop : -1.77 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 75 TYR 0.011 0.002 TYR D 415 PHE 0.013 0.001 PHE D 122 TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5597) covalent geometry : angle 0.62102 ( 7569) hydrogen bonds : bond 0.03448 ( 261) hydrogen bonds : angle 4.36163 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7633 (mp0) cc_final: 0.7355 (mp0) REVERT: D 100 LYS cc_start: 0.7819 (tttm) cc_final: 0.7549 (tttm) REVERT: D 215 LYS cc_start: 0.6711 (tptp) cc_final: 0.6466 (tptm) REVERT: D 229 MET cc_start: 0.5550 (tpt) cc_final: 0.5253 (tpt) REVERT: D 249 GLN cc_start: 0.7586 (pp30) cc_final: 0.7332 (pp30) REVERT: D 272 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: D 283 GLN cc_start: 0.6040 (tp-100) cc_final: 0.5680 (tp-100) REVERT: D 297 ILE cc_start: 0.2789 (OUTLIER) cc_final: 0.2438 (tt) REVERT: D 356 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7593 (mm) REVERT: D 359 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6583 (mm-30) REVERT: D 363 VAL cc_start: 0.8212 (m) cc_final: 0.7890 (t) REVERT: D 395 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7355 (tmtt) REVERT: D 396 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6606 (tpt-90) REVERT: D 416 GLN cc_start: 0.8649 (pp30) cc_final: 0.8284 (pm20) REVERT: E 63 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: F 69 PHE cc_start: 0.7263 (t80) cc_final: 0.6464 (t80) REVERT: F 102 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5627 (pp) REVERT: F 117 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7392 (tppp) REVERT: F 122 LYS cc_start: 0.7871 (tptt) cc_final: 0.7553 (tptt) outliers start: 32 outliers final: 20 residues processed: 125 average time/residue: 0.0850 time to fit residues: 13.0479 Evaluate side-chains 131 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 70 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.198175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.167776 restraints weight = 8910.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.172869 restraints weight = 5285.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.176578 restraints weight = 3445.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.178910 restraints weight = 2429.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.180958 restraints weight = 1841.995| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5597 Z= 0.136 Angle : 0.626 13.961 7569 Z= 0.317 Chirality : 0.044 0.177 889 Planarity : 0.004 0.055 1008 Dihedral : 6.696 59.344 799 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.83 % Allowed : 16.90 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.32), residues: 723 helix: 1.46 (0.30), residues: 309 sheet: -0.59 (0.58), residues: 84 loop : -1.72 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 78 TYR 0.011 0.002 TYR E 172 PHE 0.013 0.001 PHE D 122 TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5597) covalent geometry : angle 0.62646 ( 7569) hydrogen bonds : bond 0.03388 ( 261) hydrogen bonds : angle 4.35062 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 90 GLU cc_start: 0.7615 (mp0) cc_final: 0.7308 (mp0) REVERT: D 100 LYS cc_start: 0.7800 (tttm) cc_final: 0.7532 (tttm) REVERT: D 215 LYS cc_start: 0.6731 (tptp) cc_final: 0.6477 (tptm) REVERT: D 229 MET cc_start: 0.5550 (tpt) cc_final: 0.5261 (tpt) REVERT: D 249 GLN cc_start: 0.7597 (pp30) cc_final: 0.7338 (pp30) REVERT: D 272 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6420 (pm20) REVERT: D 283 GLN cc_start: 0.6091 (tp-100) cc_final: 0.5724 (tp-100) REVERT: D 297 ILE cc_start: 0.2635 (OUTLIER) cc_final: 0.2305 (tt) REVERT: D 356 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7577 (mm) REVERT: D 359 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6568 (mm-30) REVERT: D 395 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7342 (tmtt) REVERT: D 396 ARG cc_start: 0.6997 (tpt170) cc_final: 0.6651 (tpt-90) REVERT: D 416 GLN cc_start: 0.8686 (pp30) cc_final: 0.8292 (pm20) REVERT: E 63 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: F 69 PHE cc_start: 0.7220 (t80) cc_final: 0.6452 (t80) REVERT: F 102 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5594 (pp) REVERT: F 122 LYS cc_start: 0.7898 (tptt) cc_final: 0.7537 (tptt) outliers start: 28 outliers final: 19 residues processed: 128 average time/residue: 0.0808 time to fit residues: 12.8457 Evaluate side-chains 130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.196877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.166106 restraints weight = 8867.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.171202 restraints weight = 5269.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.174947 restraints weight = 3450.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.177289 restraints weight = 2434.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179232 restraints weight = 1855.214| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5597 Z= 0.170 Angle : 0.674 13.491 7569 Z= 0.345 Chirality : 0.044 0.154 889 Planarity : 0.005 0.051 1008 Dihedral : 6.469 58.509 795 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.66 % Allowed : 17.24 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.32), residues: 723 helix: 1.30 (0.29), residues: 310 sheet: -0.53 (0.57), residues: 89 loop : -1.76 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 78 TYR 0.010 0.002 TYR E 172 PHE 0.014 0.001 PHE D 122 TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5597) covalent geometry : angle 0.67397 ( 7569) hydrogen bonds : bond 0.03674 ( 261) hydrogen bonds : angle 4.46391 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.32 seconds wall clock time: 17 minutes 26.95 seconds (1046.95 seconds total)