Starting phenix.real_space_refine on Thu Mar 6 07:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6j_35199/03_2025/8i6j_35199.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 3318 2.51 5 N 925 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5287 Number of models: 1 Model: "" Number of chains: 3 Chain: "Q" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3889 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.68 Number of scatterers: 5287 At special positions: 0 Unit cell: (97.18, 74.58, 118.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1006 8.00 N 925 7.00 C 3318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 574.3 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 50.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'Q' and resid 65 through 81 Processing helix chain 'Q' and resid 82 through 84 No H-bonds generated for 'chain 'Q' and resid 82 through 84' Processing helix chain 'Q' and resid 128 through 141 removed outlier: 4.112A pdb=" N GLN Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 185 removed outlier: 4.529A pdb=" N PHE Q 184 " --> pdb=" O GLY Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 200 removed outlier: 3.666A pdb=" N LEU Q 194 " --> pdb=" O THR Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 231 removed outlier: 3.860A pdb=" N LYS Q 231 " --> pdb=" O SER Q 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 removed outlier: 4.281A pdb=" N ASN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.567A pdb=" N ILE C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 4.008A pdb=" N SER C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 108 removed outlier: 3.985A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 removed outlier: 4.645A pdb=" N LEU C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.542A pdb=" N LYS C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 160 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.847A pdb=" N GLN C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.731A pdb=" N ASP C 211 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 212 " --> pdb=" O ILE C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.549A pdb=" N SER C 252 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.932A pdb=" N PHE C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.745A pdb=" N GLN C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 381 through 404 removed outlier: 3.761A pdb=" N LEU C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.931A pdb=" N TYR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 456 removed outlier: 4.126A pdb=" N ARG C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 3.686A pdb=" N LEU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 519 removed outlier: 3.858A pdb=" N ILE C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.735A pdb=" N PHE Q 167 " --> pdb=" O LEU Q 117 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE Q 166 " --> pdb=" O GLN Q 177 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN Q 177 " --> pdb=" O ILE Q 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL Q 168 " --> pdb=" O LYS Q 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'C' and resid 201 through 205 removed outlier: 3.680A pdb=" N ILE C 204 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 378 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 375 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 218 through 220 removed outlier: 3.504A pdb=" N ILE C 363 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 350 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 233 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.615A pdb=" N ILE C 291 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 290 " --> pdb=" O ILE C 312 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.52 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: 1769 1.34 - 1.46: 950 1.46 - 1.58: 2578 1.58 - 1.70: 3 1.70 - 1.81: 60 Bond restraints: 5360 Sorted by residual: bond pdb=" CG GLU C 511 " pdb=" CD GLU C 511 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CG GLU Q 195 " pdb=" CD GLU Q 195 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 8.77e-01 bond pdb=" CG ARG Q 225 " pdb=" CD ARG Q 225 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.66e-01 bond pdb=" N GLN Q 122 " pdb=" CA GLN Q 122 " ideal model delta sigma weight residual 1.456 1.466 -0.010 1.23e-02 6.61e+03 6.28e-01 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 6984 1.62 - 3.23: 193 3.23 - 4.85: 42 4.85 - 6.47: 14 6.47 - 8.08: 4 Bond angle restraints: 7237 Sorted by residual: angle pdb=" N ILE C 195 " pdb=" CA ILE C 195 " pdb=" C ILE C 195 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" N GLU C 511 " pdb=" CA GLU C 511 " pdb=" CB GLU C 511 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.13e+01 angle pdb=" N MET Q 73 " pdb=" CA MET Q 73 " pdb=" CB MET Q 73 " ideal model delta sigma weight residual 110.28 115.16 -4.88 1.55e+00 4.16e-01 9.91e+00 angle pdb=" N GLU Q 195 " pdb=" CA GLU Q 195 " pdb=" CB GLU Q 195 " ideal model delta sigma weight residual 110.12 114.56 -4.44 1.47e+00 4.63e-01 9.13e+00 angle pdb=" N TYR Q 102 " pdb=" CA TYR Q 102 " pdb=" C TYR Q 102 " ideal model delta sigma weight residual 110.80 116.86 -6.06 2.13e+00 2.20e-01 8.11e+00 ... (remaining 7232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 3189 27.12 - 54.23: 131 54.23 - 81.35: 9 81.35 - 108.46: 5 108.46 - 135.58: 1 Dihedral angle restraints: 3335 sinusoidal: 1393 harmonic: 1942 Sorted by residual: dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual 300.00 164.42 135.58 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA ILE Q 150 " pdb=" C ILE Q 150 " pdb=" N SER Q 151 " pdb=" CA SER Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR Q 169 " pdb=" C TYR Q 169 " pdb=" N LEU Q 170 " pdb=" CA LEU Q 170 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 514 0.032 - 0.065: 209 0.065 - 0.097: 69 0.097 - 0.129: 47 0.129 - 0.162: 7 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE C 374 " pdb=" CA ILE C 374 " pdb=" CG1 ILE C 374 " pdb=" CG2 ILE C 374 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA GLU C 511 " pdb=" N GLU C 511 " pdb=" C GLU C 511 " pdb=" CB GLU C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA TYR Q 102 " pdb=" N TYR Q 102 " pdb=" C TYR Q 102 " pdb=" CB TYR Q 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 843 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 112 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.47e+00 pdb=" CG PHE C 112 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 112 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 112 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 112 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 124 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO Q 125 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Q 125 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Q 125 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 507 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LYS C 507 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS C 507 " 0.009 2.00e-02 2.50e+03 pdb=" N THR C 508 " 0.008 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1164 2.79 - 3.32: 5151 3.32 - 3.85: 7858 3.85 - 4.37: 8250 4.37 - 4.90: 14508 Nonbonded interactions: 36931 Sorted by model distance: nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 437 " model vdw 2.265 3.040 nonbonded pdb=" O VAL Q 183 " pdb=" NZ LYS Q 197 " model vdw 2.292 3.120 nonbonded pdb=" OE1 GLU C 497 " pdb=" NZ LYS C 502 " model vdw 2.341 3.120 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.344 3.120 nonbonded pdb=" O SER C 158 " pdb=" OG1 THR C 161 " model vdw 2.348 3.040 ... (remaining 36926 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 0.029 5360 Z= 0.196 Angle : 0.697 8.081 7237 Z= 0.359 Chirality : 0.046 0.162 846 Planarity : 0.004 0.040 921 Dihedral : 14.716 135.578 2075 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.33), residues: 666 helix: 1.57 (0.31), residues: 306 sheet: -0.75 (0.66), residues: 70 loop : -3.23 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 435 HIS 0.004 0.001 HIS C 111 PHE 0.032 0.002 PHE C 112 TYR 0.011 0.002 TYR Q 102 ARG 0.009 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7745 (mmt) cc_final: 0.7351 (mmm) REVERT: C 190 ARG cc_start: 0.7336 (mmp80) cc_final: 0.7102 (mmp80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1974 time to fit residues: 20.9738 Evaluate side-chains 75 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.208966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163463 restraints weight = 7943.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149773 restraints weight = 10436.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150255 restraints weight = 10161.129| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5360 Z= 0.305 Angle : 0.717 9.055 7237 Z= 0.363 Chirality : 0.047 0.155 846 Planarity : 0.004 0.043 921 Dihedral : 7.347 135.221 736 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.20 % Allowed : 11.00 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.33), residues: 666 helix: 1.48 (0.31), residues: 311 sheet: -0.66 (0.66), residues: 70 loop : -3.31 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.006 0.001 HIS C 74 PHE 0.018 0.002 PHE Q 167 TYR 0.015 0.002 TYR C 247 ARG 0.003 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 86 LYS cc_start: 0.7448 (mttt) cc_final: 0.7106 (mmtt) REVERT: C 69 GLU cc_start: 0.7177 (tp30) cc_final: 0.6889 (tp30) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.1892 time to fit residues: 20.4334 Evaluate side-chains 83 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.213656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176677 restraints weight = 8275.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175339 restraints weight = 14835.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176902 restraints weight = 12246.707| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5360 Z= 0.158 Angle : 0.612 6.248 7237 Z= 0.307 Chirality : 0.043 0.147 846 Planarity : 0.003 0.041 921 Dihedral : 7.074 135.797 736 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.37 % Allowed : 15.64 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 666 helix: 1.66 (0.30), residues: 311 sheet: -0.33 (0.67), residues: 70 loop : -3.26 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 435 HIS 0.001 0.001 HIS C 226 PHE 0.010 0.001 PHE C 362 TYR 0.011 0.001 TYR C 247 ARG 0.004 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7745 (mmt) cc_final: 0.7373 (mmm) REVERT: C 128 LYS cc_start: 0.8310 (pptt) cc_final: 0.7810 (pptt) REVERT: C 190 ARG cc_start: 0.7203 (mmp80) cc_final: 0.6935 (mmp80) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.2412 time to fit residues: 28.1895 Evaluate side-chains 78 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN ** C 442 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 = 0.4462 r_free = 0.4462 target = 0.210375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181256 restraints weight = 8466.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179324 restraints weight = 16711.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176192 restraints weight = 8708.740| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5360 Z= 0.217 Angle : 0.651 7.173 7237 Z= 0.326 Chirality : 0.045 0.148 846 Planarity : 0.004 0.042 921 Dihedral : 7.121 135.138 736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.58 % Allowed : 16.32 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.33), residues: 666 helix: 1.65 (0.30), residues: 312 sheet: -0.38 (0.67), residues: 71 loop : -3.24 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.020 0.002 PHE Q 167 TYR 0.012 0.002 TYR C 247 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8062 (pt) REVERT: C 402 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.5064 (mt) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.1694 time to fit residues: 19.2520 Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.211211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.174208 restraints weight = 8237.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173018 restraints weight = 13320.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174175 restraints weight = 12368.009| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5360 Z= 0.192 Angle : 0.632 8.404 7237 Z= 0.315 Chirality : 0.044 0.144 846 Planarity : 0.004 0.042 921 Dihedral : 7.063 134.732 736 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.75 % Allowed : 16.84 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.33), residues: 666 helix: 1.70 (0.30), residues: 312 sheet: -0.67 (0.74), residues: 56 loop : -2.97 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.015 0.002 PHE Q 167 TYR 0.013 0.002 TYR C 247 ARG 0.007 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8065 (pptt) cc_final: 0.7548 (pptt) REVERT: C 190 ARG cc_start: 0.7279 (mmp80) cc_final: 0.6919 (mmp80) REVERT: C 376 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (pt) REVERT: C 402 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.5579 (mt) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.1729 time to fit residues: 18.6215 Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.210136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175178 restraints weight = 8212.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.178980 restraints weight = 13895.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.178360 restraints weight = 7687.327| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5360 Z= 0.214 Angle : 0.648 9.113 7237 Z= 0.322 Chirality : 0.044 0.149 846 Planarity : 0.004 0.042 921 Dihedral : 7.072 134.268 736 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.26 % Allowed : 17.53 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.33), residues: 666 helix: 1.70 (0.30), residues: 312 sheet: -0.36 (0.67), residues: 71 loop : -3.25 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.017 0.002 PHE Q 167 TYR 0.021 0.002 TYR C 247 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7784 (mmt) cc_final: 0.7550 (mmm) REVERT: C 128 LYS cc_start: 0.8015 (pptt) cc_final: 0.7568 (pptt) REVERT: C 376 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7974 (pt) REVERT: C 402 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.5695 (mt) outliers start: 19 outliers final: 15 residues processed: 90 average time/residue: 0.1770 time to fit residues: 21.0179 Evaluate side-chains 90 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175207 restraints weight = 8310.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174182 restraints weight = 13075.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175184 restraints weight = 13621.843| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5360 Z= 0.173 Angle : 0.640 9.315 7237 Z= 0.317 Chirality : 0.043 0.142 846 Planarity : 0.003 0.041 921 Dihedral : 6.964 133.723 736 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.58 % Allowed : 19.24 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.33), residues: 666 helix: 1.75 (0.30), residues: 312 sheet: -0.61 (0.74), residues: 56 loop : -2.97 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE Q 167 TYR 0.019 0.002 TYR C 437 ARG 0.007 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8224 (pptt) cc_final: 0.7995 (pptt) REVERT: C 376 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7851 (pt) REVERT: C 402 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.5929 (tt) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.1729 time to fit residues: 18.9350 Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.172536 restraints weight = 8226.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173229 restraints weight = 13330.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.174231 restraints weight = 11681.757| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 0.003 0.031 5360 Z= 0.206 Angle : 0.667 9.744 7237 Z= 0.331 Chirality : 0.044 0.149 846 Planarity : 0.004 0.041 921 Dihedral : 7.015 133.184 736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.09 % Allowed : 19.42 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.34), residues: 666 helix: 1.77 (0.30), residues: 312 sheet: -0.26 (0.68), residues: 71 loop : -3.22 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.015 0.002 PHE Q 167 TYR 0.019 0.002 TYR C 437 ARG 0.008 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7960 (pt) REVERT: C 402 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.5585 (mt) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.1669 time to fit residues: 19.4331 Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 0.0170 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.211880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.178421 restraints weight = 8249.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181002 restraints weight = 14460.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.179246 restraints weight = 7746.907| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5360 Z= 0.177 Angle : 0.668 9.521 7237 Z= 0.329 Chirality : 0.043 0.142 846 Planarity : 0.003 0.039 921 Dihedral : 6.939 132.383 736 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.92 % Allowed : 20.10 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.34), residues: 666 helix: 1.83 (0.30), residues: 311 sheet: -0.45 (0.75), residues: 55 loop : -2.99 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.001 0.001 HIS C 470 PHE 0.012 0.001 PHE C 264 TYR 0.017 0.001 TYR C 437 ARG 0.008 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 ARG cc_start: 0.7098 (mmp80) cc_final: 0.6732 (mmp80) REVERT: C 376 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7999 (pt) REVERT: C 402 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.5462 (mt) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.1688 time to fit residues: 19.5456 Evaluate side-chains 89 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.210420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174075 restraints weight = 8256.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177302 restraints weight = 14346.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177898 restraints weight = 8911.902| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5360 Z= 0.221 Angle : 0.690 8.541 7237 Z= 0.343 Chirality : 0.045 0.149 846 Planarity : 0.004 0.038 921 Dihedral : 7.000 131.795 736 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.58 % Allowed : 20.62 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.34), residues: 666 helix: 1.70 (0.30), residues: 312 sheet: -0.27 (0.68), residues: 71 loop : -3.26 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.016 0.002 PHE Q 167 TYR 0.019 0.002 TYR C 437 ARG 0.009 0.000 ARG Q 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.6786 (mtt) cc_final: 0.6047 (mtt) REVERT: C 402 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.5590 (mt) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1674 time to fit residues: 19.4632 Evaluate side-chains 91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.0470 chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 0.0010 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 overall best weight: 0.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.213818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.176918 restraints weight = 8307.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176722 restraints weight = 13220.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177480 restraints weight = 12945.925| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5360 Z= 0.164 Angle : 0.674 11.046 7237 Z= 0.335 Chirality : 0.043 0.147 846 Planarity : 0.003 0.039 921 Dihedral : 6.808 130.776 736 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.06 % Allowed : 21.31 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.34), residues: 666 helix: 1.85 (0.31), residues: 311 sheet: -0.52 (0.74), residues: 56 loop : -2.99 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.014 0.001 PHE C 264 TYR 0.022 0.002 TYR C 437 ARG 0.009 0.000 ARG Q 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.34 seconds wall clock time: 31 minutes 26.46 seconds (1886.46 seconds total)