Starting phenix.real_space_refine on Sat May 10 06:31:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6j_35199/05_2025/8i6j_35199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6j_35199/05_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_35199/05_2025/8i6j_35199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6j_35199/05_2025/8i6j_35199.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6j_35199/05_2025/8i6j_35199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6j_35199/05_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-5687/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: 3.91, per 1000 atoms: 0.74 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 629.8 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: 0.44 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: 1.18 Time building geometry restraints manager: 1.48 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.560 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.880 ------------------------------------------------------------------------------- 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= 0.140 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 Details of bonding type rmsd hydrogen bonds : bond 0.15313 ( 236) hydrogen bonds : angle 5.57275 ( 681) covalent geometry : bond 0.00303 ( 5360) covalent geometry : angle 0.69743 ( 7237) *********************** 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 : 0.613 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: 0.2016 time to fit residues: 21.3439 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 : 0.621 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163546 restraints weight = 7943.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150128 restraints weight = 9248.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150833 restraints weight = 9103.980| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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= 0.200 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 Details of bonding type rmsd hydrogen bonds : bond 0.06107 ( 236) hydrogen bonds : angle 4.53126 ( 681) covalent geometry : bond 0.00474 ( 5360) covalent geometry : angle 0.71746 ( 7237) *********************** 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 : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 86 LYS cc_start: 0.7451 (mttt) cc_final: 0.7122 (mmtt) REVERT: C 69 GLU cc_start: 0.7179 (tp30) cc_final: 0.6892 (tp30) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.1778 time to fit residues: 19.1381 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 : 0.549 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 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: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.213369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176355 restraints weight = 8282.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175330 restraints weight = 15214.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176734 restraints weight = 12376.857| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1505 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= 0.116 Angle : 0.615 6.327 7237 Z= 0.308 Chirality : 0.044 0.148 846 Planarity : 0.003 0.042 921 Dihedral : 7.089 135.851 736 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.72 % Allowed : 15.29 % 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: -0.78 (0.33), residues: 666 helix: 1.65 (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 0.012 0.001 TRP C 435 HIS 0.002 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 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 236) hydrogen bonds : angle 4.02640 ( 681) covalent geometry : bond 0.00251 ( 5360) covalent geometry : angle 0.61467 ( 7237) *********************** 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 94 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8287 (pptt) cc_final: 0.7803 (pptt) REVERT: C 190 ARG cc_start: 0.7219 (mmp80) cc_final: 0.6952 (mmp80) REVERT: C 376 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (pt) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.1756 time to fit residues: 20.0110 Evaluate side-chains 79 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 376 LEU 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: 0.1980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.210813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174947 restraints weight = 8463.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177052 restraints weight = 16258.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178258 restraints weight = 10219.010| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1756 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= 0.139 Angle : 0.640 6.894 7237 Z= 0.321 Chirality : 0.044 0.146 846 Planarity : 0.004 0.042 921 Dihedral : 7.106 135.156 736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.75 % Allowed : 16.15 % 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: -0.75 (0.33), residues: 666 helix: 1.65 (0.30), residues: 312 sheet: -0.36 (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 0.019 0.002 PHE Q 167 TYR 0.013 0.002 TYR C 247 ARG 0.005 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 236) hydrogen bonds : angle 4.10090 ( 681) covalent geometry : bond 0.00315 ( 5360) covalent geometry : angle 0.64043 ( 7237) *********************** 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 91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8082 (pt) REVERT: C 402 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.5786 (tt) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.1678 time to fit residues: 18.5918 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 : 0.607 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 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 = 0.4443 r_free = 0.4443 target = 0.208253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165451 restraints weight = 8267.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162905 restraints weight = 10896.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156230 restraints weight = 8345.267| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5360 Z= 0.178 Angle : 0.688 8.782 7237 Z= 0.346 Chirality : 0.046 0.192 846 Planarity : 0.004 0.046 921 Dihedral : 7.255 134.991 736 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.44 % Allowed : 16.84 % Favored : 79.73 % 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: -0.87 (0.33), residues: 666 helix: 1.58 (0.30), residues: 312 sheet: -0.51 (0.67), residues: 71 loop : -3.31 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.023 0.002 PHE Q 167 TYR 0.012 0.002 TYR C 247 ARG 0.006 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.05549 ( 236) hydrogen bonds : angle 4.18876 ( 681) covalent geometry : bond 0.00416 ( 5360) covalent geometry : angle 0.68829 ( 7237) *********************** 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 95 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8203 (pptt) cc_final: 0.7598 (pptt) REVERT: C 376 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8153 (pt) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1609 time to fit residues: 18.2493 Evaluate side-chains 91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP 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 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 188 ASN Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 391 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: 5.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.211379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174223 restraints weight = 8251.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176542 restraints weight = 14740.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177305 restraints weight = 10786.558| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2033 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= 0.121 Angle : 0.626 7.580 7237 Z= 0.311 Chirality : 0.044 0.143 846 Planarity : 0.003 0.042 921 Dihedral : 7.074 135.522 736 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.23 % Allowed : 19.42 % Favored : 78.35 % 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: -0.69 (0.34), residues: 666 helix: 1.70 (0.31), residues: 312 sheet: -0.16 (0.68), residues: 70 loop : -3.25 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 74 PHE 0.013 0.001 PHE Q 167 TYR 0.021 0.002 TYR C 247 ARG 0.005 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 236) hydrogen bonds : angle 3.96617 ( 681) covalent geometry : bond 0.00270 ( 5360) covalent geometry : angle 0.62618 ( 7237) *********************** 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 88 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7792 (mmt) cc_final: 0.7563 (mmm) REVERT: C 128 LYS cc_start: 0.8068 (pptt) cc_final: 0.7600 (pptt) REVERT: C 152 MET cc_start: 0.6623 (mtt) cc_final: 0.6305 (mtt) REVERT: C 402 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.5637 (mt) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.1680 time to fit residues: 18.5719 Evaluate side-chains 85 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.212184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.173622 restraints weight = 8336.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172765 restraints weight = 13533.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174043 restraints weight = 12102.342| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2093 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= 0.115 Angle : 0.624 7.348 7237 Z= 0.309 Chirality : 0.043 0.143 846 Planarity : 0.003 0.042 921 Dihedral : 6.985 134.649 736 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.58 % Allowed : 19.93 % 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: 1.75 (0.30), residues: 312 sheet: -0.56 (0.75), residues: 56 loop : -2.99 (0.31), residues: 298 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 0.011 0.001 PHE Q 167 TYR 0.019 0.002 TYR C 437 ARG 0.007 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 236) hydrogen bonds : angle 3.90760 ( 681) covalent geometry : bond 0.00255 ( 5360) covalent geometry : angle 0.62426 ( 7237) *********************** 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 : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7672 (mmt) cc_final: 0.7377 (mmm) REVERT: C 128 LYS cc_start: 0.8217 (pptt) cc_final: 0.7980 (pptt) REVERT: C 376 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7886 (pt) REVERT: C 402 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.5994 (tt) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 0.1626 time to fit residues: 17.9758 Evaluate side-chains 86 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.212383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.175759 restraints weight = 8007.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177348 restraints weight = 15757.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.178493 restraints weight = 11239.845| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2167 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= 0.126 Angle : 0.631 7.506 7237 Z= 0.313 Chirality : 0.044 0.146 846 Planarity : 0.003 0.041 921 Dihedral : 6.965 133.521 736 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.58 % Allowed : 19.93 % 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: -0.59 (0.34), residues: 666 helix: 1.81 (0.31), residues: 312 sheet: -0.60 (0.75), residues: 56 loop : -2.97 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.002 0.001 HIS C 74 PHE 0.014 0.001 PHE Q 167 TYR 0.018 0.002 TYR C 437 ARG 0.007 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 236) hydrogen bonds : angle 3.93865 ( 681) covalent geometry : bond 0.00285 ( 5360) covalent geometry : angle 0.63111 ( 7237) *********************** 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 88 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7765 (mmt) cc_final: 0.7481 (mmm) REVERT: C 376 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 402 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.5679 (mt) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.1581 time to fit residues: 17.5291 Evaluate side-chains 85 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 62 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 = 0.4501 r_free = 0.4501 target = 0.214282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179661 restraints weight = 8267.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181737 restraints weight = 14767.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.181719 restraints weight = 8046.871| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5360 Z= 0.106 Angle : 0.622 9.199 7237 Z= 0.304 Chirality : 0.043 0.134 846 Planarity : 0.003 0.039 921 Dihedral : 6.835 132.064 736 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.75 % Allowed : 20.45 % 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: -0.50 (0.34), residues: 666 helix: 1.93 (0.31), residues: 311 sheet: -0.50 (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 0.001 0.000 HIS C 420 PHE 0.010 0.001 PHE C 264 TYR 0.017 0.001 TYR C 437 ARG 0.008 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 236) hydrogen bonds : angle 3.87110 ( 681) covalent geometry : bond 0.00228 ( 5360) covalent geometry : angle 0.62160 ( 7237) *********************** 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: 16 poor density : 78 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 102 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.5692 (p90) REVERT: Q 205 MET cc_start: 0.8225 (tmm) cc_final: 0.7975 (tmm) REVERT: C 190 ARG cc_start: 0.7100 (mmp80) cc_final: 0.6749 (mmp80) REVERT: C 280 GLU cc_start: 0.7443 (tp30) cc_final: 0.7003 (mp0) REVERT: C 376 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (pt) REVERT: C 402 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5919 (tt) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.1626 time to fit residues: 19.3138 Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 102 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 58 optimal weight: 0.0040 chunk 21 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.213548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.177186 restraints weight = 8325.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178770 restraints weight = 13351.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179465 restraints weight = 10100.209| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5360 Z= 0.113 Angle : 0.635 8.646 7237 Z= 0.313 Chirality : 0.043 0.139 846 Planarity : 0.004 0.039 921 Dihedral : 6.747 130.554 736 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.41 % Allowed : 21.31 % Favored : 76.29 % 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: -0.50 (0.33), residues: 666 helix: 1.91 (0.30), residues: 311 sheet: -0.43 (0.74), residues: 56 loop : -2.97 (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 118 PHE 0.011 0.001 PHE C 264 TYR 0.019 0.001 TYR C 437 ARG 0.009 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 236) hydrogen bonds : angle 3.86866 ( 681) covalent geometry : bond 0.00251 ( 5360) covalent geometry : angle 0.63491 ( 7237) ********************** 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 90 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 102 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5621 (p90) REVERT: C 190 ARG cc_start: 0.7174 (mmp80) cc_final: 0.6813 (mmp80) REVERT: C 280 GLU cc_start: 0.7510 (tp30) cc_final: 0.7068 (mp0) REVERT: C 376 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7893 (pt) REVERT: C 402 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.5890 (tt) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.1574 time to fit residues: 18.3918 Evaluate side-chains 86 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 102 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.212041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.178233 restraints weight = 8379.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181956 restraints weight = 15044.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181608 restraints weight = 9826.517| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5360 Z= 0.121 Angle : 0.645 8.400 7237 Z= 0.318 Chirality : 0.044 0.144 846 Planarity : 0.004 0.038 921 Dihedral : 6.649 128.655 736 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.92 % Allowed : 20.96 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.34), residues: 666 helix: 1.87 (0.30), residues: 312 sheet: -0.55 (0.69), residues: 63 loop : -3.03 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.012 0.002 PHE Q 167 TYR 0.019 0.001 TYR C 437 ARG 0.009 0.000 ARG Q 225 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 236) hydrogen bonds : angle 3.92870 ( 681) covalent geometry : bond 0.00273 ( 5360) covalent geometry : angle 0.64541 ( 7237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.76 seconds wall clock time: 33 minutes 1.70 seconds (1981.70 seconds total)