Starting phenix.real_space_refine on Tue Mar 11 14:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2025/7m3l_23656.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3875 2.51 5 N 1044 2.21 5 O 1171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6113 Number of models: 1 Model: "" Number of chains: 3 Chain: "A1" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4347 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 506} Chain: "L2" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "H2" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 5.08, per 1000 atoms: 0.83 Number of scatterers: 6113 At special positions: 0 Unit cell: (91.528, 104.988, 110.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1171 8.00 N 1044 7.00 C 3875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSL2 23 " - pdb=" SG CYSL2 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 22 " - pdb=" SG CYSH2 95 " distance=2.02 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: 1.55 Conformation dependent library (CDL) restraints added in 875.4 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 6.1% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A1' and resid 116 through 120 removed outlier: 3.617A pdb=" N VALA1 119 " --> pdb=" O ALAA1 116 " (cutoff:3.500A) Processing helix chain 'A1' and resid 122 through 126 removed outlier: 3.515A pdb=" N TRPA1 126 " --> pdb=" O PROA1 123 " (cutoff:3.500A) Processing helix chain 'A1' and resid 309 through 313 removed outlier: 3.846A pdb=" N ARGA1 313 " --> pdb=" O GLNA1 310 " (cutoff:3.500A) Processing helix chain 'A1' and resid 409 through 413 removed outlier: 3.581A pdb=" N ASPA1 413 " --> pdb=" O PROA1 410 " (cutoff:3.500A) Processing helix chain 'A1' and resid 425 through 427 No H-bonds generated for 'chain 'A1' and resid 425 through 427' Processing helix chain 'A1' and resid 443 through 447 Processing helix chain 'A1' and resid 554 through 558 removed outlier: 3.935A pdb=" N GLNA1 558 " --> pdb=" O VALA1 555 " (cutoff:3.500A) Processing helix chain 'L2' and resid 79 through 83 removed outlier: 3.871A pdb=" N LEUL2 83 " --> pdb=" O ALAL2 80 " (cutoff:3.500A) Processing helix chain 'H2' and resid 28 through 32 removed outlier: 3.564A pdb=" N ASNH2 31 " --> pdb=" O THRH2 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYRH2 32 " --> pdb=" O PHEH2 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 28 through 32' Processing helix chain 'H2' and resid 62 through 65 removed outlier: 3.960A pdb=" N LYSH2 65 " --> pdb=" O GLUH2 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A1' and resid 49 through 53 removed outlier: 8.280A pdb=" N ASPA1 526 " --> pdb=" O PHEA1 146 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHEA1 146 " --> pdb=" O ASPA1 526 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRPA1 528 " --> pdb=" O GLUA1 144 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLUA1 144 " --> pdb=" O TRPA1 528 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYSA1 530 " --> pdb=" O GLUA1 142 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLUA1 142 " --> pdb=" O LYSA1 530 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYSA1 532 " --> pdb=" O SERA1 140 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SERA1 140 " --> pdb=" O LYSA1 532 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VALA1 534 " --> pdb=" O LEUA1 138 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEUA1 138 " --> pdb=" O VALA1 534 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYSA1 536 " --> pdb=" O LEUA1 136 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEUA1 136 " --> pdb=" O LYSA1 536 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYSA1 538 " --> pdb=" O SERA1 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A1' and resid 163 through 167 removed outlier: 8.280A pdb=" N ASPA1 526 " --> pdb=" O PHEA1 146 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHEA1 146 " --> pdb=" O ASPA1 526 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRPA1 528 " --> pdb=" O GLUA1 144 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLUA1 144 " --> pdb=" O TRPA1 528 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYSA1 530 " --> pdb=" O GLUA1 142 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLUA1 142 " --> pdb=" O LYSA1 530 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYSA1 532 " --> pdb=" O SERA1 140 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SERA1 140 " --> pdb=" O LYSA1 532 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VALA1 534 " --> pdb=" O LEUA1 138 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEUA1 138 " --> pdb=" O VALA1 534 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYSA1 536 " --> pdb=" O LEUA1 136 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEUA1 136 " --> pdb=" O LYSA1 536 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYSA1 538 " --> pdb=" O SERA1 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A1' and resid 82 through 84 removed outlier: 6.851A pdb=" N ILEA1 105 " --> pdb=" O PHEA1 212 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHEA1 212 " --> pdb=" O ILEA1 105 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THRA1 107 " --> pdb=" O TYRA1 210 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N TYRA1 210 " --> pdb=" O THRA1 107 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRPA1 109 " --> pdb=" O TRPA1 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A1' and resid 82 through 84 removed outlier: 5.866A pdb=" N VALA1 502 " --> pdb=" O PROA1 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A1' and resid 215 through 218 removed outlier: 3.666A pdb=" N GLYA1 235 " --> pdb=" O ASPA1 215 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THRA1 217 " --> pdb=" O TYRA1 233 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYRA1 233 " --> pdb=" O THRA1 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A1' and resid 276 through 278 Processing sheet with id=AA7, first strand: chain 'A1' and resid 335 through 336 removed outlier: 6.306A pdb=" N GLUA1 335 " --> pdb=" O ALAA1 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A1' and resid 345 through 346 Processing sheet with id=AA9, first strand: chain 'A1' and resid 377 through 380 Processing sheet with id=AB1, first strand: chain 'A1' and resid 415 through 416 Processing sheet with id=AB2, first strand: chain 'A1' and resid 470 through 472 removed outlier: 6.811A pdb=" N ASPA1 471 " --> pdb=" O CYSA1 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L2' and resid 4 through 6 removed outlier: 5.679A pdb=" N THRL2 69 " --> pdb=" O ALAL2 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L2' and resid 10 through 13 removed outlier: 6.333A pdb=" N LEUL2 33 " --> pdb=" O TYRL2 49 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYRL2 49 " --> pdb=" O LEUL2 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRPL2 35 " --> pdb=" O LEUL2 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H2' and resid 3 through 6 removed outlier: 3.709A pdb=" N THRH2 78 " --> pdb=" O ASPH2 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H2' and resid 57 through 60 removed outlier: 3.653A pdb=" N SERH2 57 " --> pdb=" O PHEH2 52 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRPH2 36 " --> pdb=" O ILEH2 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TRPH2 50 " --> pdb=" O METH2 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N METH2 34 " --> pdb=" O TRPH2 50 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 288 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: 1.91 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1209 1.32 - 1.44: 1659 1.44 - 1.56: 3380 1.56 - 1.68: 0 1.68 - 1.81: 38 Bond restraints: 6286 Sorted by residual: bond pdb=" CA ASNA1 115 " pdb=" CB ASNA1 115 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.51e-02 4.39e+03 9.56e+00 bond pdb=" CB VALA1 130 " pdb=" CG2 VALA1 130 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.77e+00 bond pdb=" C LEUA1 422 " pdb=" N PROA1 423 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.01e+00 bond pdb=" CB CYSH2 95 " pdb=" SG CYSH2 95 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" N GLNA1 127 " pdb=" CA GLNA1 127 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.85e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 8470 3.24 - 6.48: 96 6.48 - 9.72: 11 9.72 - 12.97: 1 12.97 - 16.21: 1 Bond angle restraints: 8579 Sorted by residual: angle pdb=" C TRPA1 126 " pdb=" N GLNA1 127 " pdb=" CA GLNA1 127 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C THRL2 31 " pdb=" N ALAL2 32 " pdb=" CA ALAL2 32 " ideal model delta sigma weight residual 122.46 129.27 -6.81 1.41e+00 5.03e-01 2.33e+01 angle pdb=" N GLNA1 127 " pdb=" CA GLNA1 127 " pdb=" C GLNA1 127 " ideal model delta sigma weight residual 110.80 119.91 -9.11 2.13e+00 2.20e-01 1.83e+01 angle pdb=" N ALAL2 32 " pdb=" CA ALAL2 32 " pdb=" C ALAL2 32 " ideal model delta sigma weight residual 111.30 116.86 -5.56 1.36e+00 5.41e-01 1.67e+01 angle pdb=" C ASNA1 421 " pdb=" N LEUA1 422 " pdb=" CA LEUA1 422 " ideal model delta sigma weight residual 121.03 127.08 -6.05 1.60e+00 3.91e-01 1.43e+01 ... (remaining 8574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3233 17.26 - 34.53: 361 34.53 - 51.79: 60 51.79 - 69.05: 11 69.05 - 86.31: 9 Dihedral angle restraints: 3674 sinusoidal: 1439 harmonic: 2235 Sorted by residual: dihedral pdb=" CA LEUA1 422 " pdb=" C LEUA1 422 " pdb=" N PROA1 423 " pdb=" CA PROA1 423 " ideal model delta harmonic sigma weight residual -180.00 -126.65 -53.35 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA TRPA1 126 " pdb=" C TRPA1 126 " pdb=" N GLNA1 127 " pdb=" CA GLNA1 127 " ideal model delta harmonic sigma weight residual 180.00 133.14 46.86 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" CA GLNA1 159 " pdb=" C GLNA1 159 " pdb=" N PROA1 160 " pdb=" CA PROA1 160 " ideal model delta harmonic sigma weight residual 180.00 140.03 39.97 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 3671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 668 0.058 - 0.115: 206 0.115 - 0.173: 40 0.173 - 0.230: 7 0.230 - 0.287: 2 Chirality restraints: 923 Sorted by residual: chirality pdb=" CB THRA1 265 " pdb=" CA THRA1 265 " pdb=" OG1 THRA1 265 " pdb=" CG2 THRA1 265 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THRA1 158 " pdb=" CA THRA1 158 " pdb=" OG1 THRA1 158 " pdb=" CG2 THRA1 158 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILEA1 330 " pdb=" CA ILEA1 330 " pdb=" CG1 ILEA1 330 " pdb=" CG2 ILEA1 330 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 920 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPH2 50 " 0.030 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRPH2 50 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRPH2 50 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRPH2 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRPH2 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRPH2 50 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRPH2 50 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRPH2 50 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRPH2 50 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRPH2 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLNA1 159 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PROA1 160 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROA1 160 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROA1 160 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEUA1 422 " -0.014 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C LEUA1 422 " 0.046 2.00e-02 2.50e+03 pdb=" O LEUA1 422 " -0.017 2.00e-02 2.50e+03 pdb=" N PROA1 423 " -0.016 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 2 2.22 - 2.89: 2424 2.89 - 3.56: 7602 3.56 - 4.23: 14149 4.23 - 4.90: 24344 Nonbonded interactions: 48521 Sorted by model distance: nonbonded pdb=" O GLYA1 227 " pdb=" CE1 HISH2 101 " model vdw 1.551 3.260 nonbonded pdb=" OD1 ASNA1 93 " pdb=" O GLYH2 102 " model vdw 1.859 3.040 nonbonded pdb=" O GLYA1 227 " pdb=" ND1 HISH2 101 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASPH2 33 " pdb=" OH TYRH2 104 " model vdw 2.297 3.040 nonbonded pdb=" OG SERL2 43 " pdb=" O GLYH2 110 " model vdw 2.307 3.040 ... (remaining 48516 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3856 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 : 0.009 0.079 6286 Z= 0.577 Angle : 0.966 16.208 8579 Z= 0.547 Chirality : 0.058 0.287 923 Planarity : 0.008 0.075 1122 Dihedral : 15.046 86.313 2240 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.10 % Favored : 90.64 % Rotamer: Outliers : 0.30 % Allowed : 10.98 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.28 % 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: -3.19 (0.25), residues: 769 helix: -4.56 (0.44), residues: 18 sheet: -1.97 (0.30), residues: 234 loop : -2.20 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRPH2 50 HIS 0.009 0.002 HISA1 403 PHE 0.020 0.003 PHEA1 45 TYR 0.030 0.003 TYRA1 342 ARG 0.006 0.001 ARGH2 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.2619 time to fit residues: 25.4430 Evaluate side-chains 39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 38 optimal weight: 0.0170 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 47 ASN A1 70 HIS A1 167 ASN A1 181 ASN ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 231 ASN A1 234 HIS ** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 384 HIS A1 403 HIS A1 416 GLN A1 419 ASN A1 466 ASN A1 468 GLN A1 483 HIS A1 550 GLN L2 37 GLN L2 53 ASN ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.055867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.048667 restraints weight = 59847.190| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 7.38 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6286 Z= 0.268 Angle : 0.701 10.244 8579 Z= 0.365 Chirality : 0.046 0.157 923 Planarity : 0.006 0.063 1122 Dihedral : 6.434 65.089 839 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 2.26 % Allowed : 15.04 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -2.35 (0.27), residues: 769 helix: -4.48 (0.74), residues: 12 sheet: -1.43 (0.31), residues: 244 loop : -1.60 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPH2 50 HIS 0.006 0.002 HISH2 101 PHE 0.015 0.002 PHEA1 266 TYR 0.013 0.001 TYRL2 92 ARG 0.004 0.001 ARGA1 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 47 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7219 (m-40) REVERT: L2 4 MET cc_start: 0.6673 (mmm) cc_final: 0.4619 (tpp) REVERT: L2 17 ASP cc_start: 0.9288 (t0) cc_final: 0.9053 (t0) REVERT: L2 24 LYS cc_start: 0.9262 (mmtm) cc_final: 0.9057 (mmmt) REVERT: H2 65 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9356 (mmmt) outliers start: 15 outliers final: 7 residues processed: 60 average time/residue: 0.2352 time to fit residues: 18.0016 Evaluate side-chains 43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 47 ASN Chi-restraints excluded: chain A1 residue 106 VAL Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 482 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 47 ASN ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 242 GLN ** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 43 GLN H2 81 GLN H2 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.057035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.049906 restraints weight = 61378.897| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 7.24 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6286 Z= 0.152 Angle : 0.586 8.172 8579 Z= 0.294 Chirality : 0.043 0.140 923 Planarity : 0.005 0.067 1122 Dihedral : 5.628 58.880 839 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 2.41 % Allowed : 15.49 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.91 (0.28), residues: 769 helix: -4.54 (0.69), residues: 12 sheet: -1.22 (0.32), residues: 229 loop : -1.24 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPH2 50 HIS 0.003 0.001 HISA1 222 PHE 0.012 0.001 PHEA1 527 TYR 0.007 0.001 TYRH2 104 ARG 0.002 0.000 ARGA1 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.6699 (mmm) cc_final: 0.4595 (tpp) outliers start: 16 outliers final: 6 residues processed: 54 average time/residue: 0.2326 time to fit residues: 16.4430 Evaluate side-chains 41 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 106 VAL Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 482 LEU Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 365 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 = 0.3827 r_free = 0.3827 target = 0.051886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.045699 restraints weight = 71484.072| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 6.55 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6286 Z= 0.292 Angle : 0.723 13.884 8579 Z= 0.362 Chirality : 0.045 0.193 923 Planarity : 0.005 0.054 1122 Dihedral : 5.846 57.783 839 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 3.76 % Allowed : 14.59 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.61 (0.29), residues: 769 helix: -4.15 (1.05), residues: 12 sheet: -0.87 (0.33), residues: 224 loop : -1.11 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPH2 50 HIS 0.007 0.002 HISL2 8 PHE 0.024 0.002 PHEA1 53 TYR 0.012 0.001 TYRA1 510 ARG 0.011 0.001 ARGL2 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8005 (mmm) cc_final: 0.7506 (tpp) REVERT: L2 24 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8982 (mmmt) REVERT: L2 47 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (mp) outliers start: 25 outliers final: 13 residues processed: 56 average time/residue: 0.2291 time to fit residues: 16.7865 Evaluate side-chains 43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 54 LEU Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 539 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 47 LEU Chi-restraints excluded: chain H2 residue 2 VAL Chi-restraints excluded: chain H2 residue 9 LEU Chi-restraints excluded: chain H2 residue 15 SER Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 51 ILE Chi-restraints excluded: chain H2 residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 143 GLN ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 446 ASN A1 468 GLN A1 560 ASN H2 39 GLN H2 81 GLN H2 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.051330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.044643 restraints weight = 65272.432| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 6.78 r_work: 0.3571 rms_B_bonded: 6.71 restraints_weight: 2.0000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6286 Z= 0.184 Angle : 0.568 8.024 8579 Z= 0.288 Chirality : 0.042 0.149 923 Planarity : 0.004 0.058 1122 Dihedral : 5.298 55.823 839 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 1.80 % Allowed : 16.39 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.28 (0.29), residues: 769 helix: -5.46 (0.44), residues: 6 sheet: -0.61 (0.32), residues: 230 loop : -0.91 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPH2 50 HIS 0.003 0.001 HISA1 222 PHE 0.008 0.001 PHEA1 527 TYR 0.008 0.001 TYRA1 510 ARG 0.004 0.000 ARGA1 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8690 (mmm) cc_final: 0.7499 (tpp) REVERT: L2 27 GLN cc_start: 0.8898 (pp30) cc_final: 0.8628 (pp30) outliers start: 12 outliers final: 5 residues processed: 43 average time/residue: 0.2550 time to fit residues: 14.3700 Evaluate side-chains 31 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 433 THR Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain L2 residue 107 LYS Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 30.0000 chunk 29 optimal weight: 0.0670 chunk 6 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 147 ASN ** A1 222 HIS ** 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 = 0.3781 r_free = 0.3781 target = 0.049696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.043525 restraints weight = 67728.677| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 6.35 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.9842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6286 Z= 0.233 Angle : 0.614 10.430 8579 Z= 0.309 Chirality : 0.042 0.145 923 Planarity : 0.004 0.049 1122 Dihedral : 5.394 55.067 839 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.50 % Favored : 93.37 % Rotamer: Outliers : 2.56 % Allowed : 16.69 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.18 (0.30), residues: 769 helix: -5.47 (0.43), residues: 6 sheet: -0.61 (0.33), residues: 235 loop : -0.80 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 PHE 0.010 0.001 PHEA1 51 TYR 0.011 0.001 TYRA1 510 ARG 0.007 0.000 ARGH2 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.7804 (mmm) cc_final: 0.7561 (mmm) REVERT: A1 319 MET cc_start: 0.5511 (mmm) cc_final: 0.5256 (mmt) REVERT: L2 4 MET cc_start: 0.8798 (mmm) cc_final: 0.8312 (tpp) REVERT: L2 24 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9411 (mmmt) outliers start: 17 outliers final: 10 residues processed: 48 average time/residue: 0.2332 time to fit residues: 14.7219 Evaluate side-chains 38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 433 THR Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 107 LYS Chi-restraints excluded: chain H2 residue 9 LEU Chi-restraints excluded: chain H2 residue 15 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 5.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 43 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 = 0.3696 r_free = 0.3696 target = 0.047886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.041074 restraints weight = 66222.648| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 7.24 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 1.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6286 Z= 0.245 Angle : 0.649 10.902 8579 Z= 0.326 Chirality : 0.043 0.166 923 Planarity : 0.005 0.061 1122 Dihedral : 5.466 53.683 839 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 3.01 % Allowed : 17.29 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.02 (0.30), residues: 769 helix: -5.47 (0.43), residues: 6 sheet: -0.48 (0.33), residues: 232 loop : -0.70 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 PHE 0.019 0.001 PHEA1 141 TYR 0.012 0.001 TYRA1 510 ARG 0.009 0.001 ARGH2 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.8708 (mmm) cc_final: 0.8428 (mmm) REVERT: A1 319 MET cc_start: 0.6376 (mmm) cc_final: 0.5967 (mmt) REVERT: A1 331 MET cc_start: 0.7597 (mmm) cc_final: 0.6873 (tmm) REVERT: L2 4 MET cc_start: 0.9007 (mmm) cc_final: 0.8803 (tpt) REVERT: H2 34 MET cc_start: 0.8668 (tpp) cc_final: 0.8344 (tpp) outliers start: 20 outliers final: 11 residues processed: 48 average time/residue: 0.2113 time to fit residues: 13.7138 Evaluate side-chains 38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 433 THR Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 88 CYS Chi-restraints excluded: chain H2 residue 9 LEU Chi-restraints excluded: chain H2 residue 15 SER Chi-restraints excluded: chain H2 residue 63 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 62 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 43 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 = 0.3661 r_free = 0.3661 target = 0.047138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.040549 restraints weight = 68223.146| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 6.94 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 1.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6286 Z= 0.270 Angle : 0.668 11.485 8579 Z= 0.331 Chirality : 0.043 0.190 923 Planarity : 0.004 0.049 1122 Dihedral : 5.453 54.430 839 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 1.65 % Allowed : 18.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -1.00 (0.30), residues: 769 helix: -5.47 (0.43), residues: 6 sheet: -0.38 (0.34), residues: 224 loop : -0.74 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPH2 50 HIS 0.005 0.001 HISA1 222 PHE 0.008 0.001 PHEA1 535 TYR 0.016 0.001 TYRA1 510 ARG 0.009 0.001 ARGH2 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 319 MET cc_start: 0.6212 (mmm) cc_final: 0.5760 (mmt) REVERT: A1 330 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8399 (tt) REVERT: A1 331 MET cc_start: 0.7360 (mmm) cc_final: 0.6859 (tmm) REVERT: A1 518 MET cc_start: 0.8180 (tpp) cc_final: 0.7947 (tpp) REVERT: L2 70 ASP cc_start: 0.9770 (p0) cc_final: 0.9568 (t0) REVERT: H2 34 MET cc_start: 0.8821 (tpp) cc_final: 0.8497 (tpp) outliers start: 11 outliers final: 9 residues processed: 39 average time/residue: 0.1947 time to fit residues: 10.3784 Evaluate side-chains 39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 330 ILE Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 433 THR Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain H2 residue 9 LEU Chi-restraints excluded: chain H2 residue 15 SER Chi-restraints excluded: chain H2 residue 63 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 0.0670 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 43 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 = 0.3666 r_free = 0.3666 target = 0.047407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.040624 restraints weight = 66219.977| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 6.77 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 1.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6286 Z= 0.186 Angle : 0.662 13.434 8579 Z= 0.324 Chirality : 0.044 0.173 923 Planarity : 0.004 0.052 1122 Dihedral : 5.172 53.167 839 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 1.35 % Allowed : 18.95 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.86 (0.31), residues: 769 helix: -5.44 (0.46), residues: 6 sheet: -0.30 (0.33), residues: 239 loop : -0.62 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 PHE 0.008 0.001 PHEA1 535 TYR 0.007 0.001 TYRA1 510 ARG 0.006 0.000 ARGH2 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 319 MET cc_start: 0.6036 (mmm) cc_final: 0.5578 (mmt) REVERT: A1 330 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A1 331 MET cc_start: 0.7450 (mmm) cc_final: 0.7232 (tmm) REVERT: L2 4 MET cc_start: 0.8811 (tpt) cc_final: 0.8396 (tpp) REVERT: H2 34 MET cc_start: 0.8840 (tpp) cc_final: 0.8544 (tpp) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.2234 time to fit residues: 11.1348 Evaluate side-chains 35 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 330 ILE Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain H2 residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 181 ASN ** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.046848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.040255 restraints weight = 70852.723| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 6.90 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 1.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6286 Z= 0.265 Angle : 0.714 15.173 8579 Z= 0.348 Chirality : 0.043 0.175 923 Planarity : 0.004 0.049 1122 Dihedral : 5.466 51.484 839 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.41 % Favored : 92.46 % Rotamer: Outliers : 0.90 % Allowed : 19.25 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.89 (0.30), residues: 769 helix: -5.45 (0.45), residues: 6 sheet: -0.24 (0.34), residues: 235 loop : -0.68 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPH2 50 HIS 0.005 0.001 HISA1 222 PHE 0.009 0.001 PHEA1 535 TYR 0.019 0.001 TYRH2 80 ARG 0.012 0.001 ARGH2 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A1 319 MET cc_start: 0.6295 (mmm) cc_final: 0.5837 (mmt) REVERT: A1 330 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8864 (tp) REVERT: L2 4 MET cc_start: 0.8703 (tpt) cc_final: 0.8369 (tpp) REVERT: L2 42 GLN cc_start: 0.9574 (mm110) cc_final: 0.9157 (mp10) REVERT: H2 34 MET cc_start: 0.8760 (tpp) cc_final: 0.8482 (tpp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1913 time to fit residues: 9.0886 Evaluate side-chains 35 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 322 THR Chi-restraints excluded: chain A1 residue 330 ILE Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 494 CYS Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain H2 residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 43 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 = 0.3655 r_free = 0.3655 target = 0.046858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.040083 restraints weight = 68235.543| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 7.06 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 1.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6286 Z= 0.209 Angle : 0.664 16.418 8579 Z= 0.326 Chirality : 0.043 0.170 923 Planarity : 0.004 0.050 1122 Dihedral : 5.188 52.177 839 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.50 % Favored : 93.37 % Rotamer: Outliers : 1.05 % Allowed : 19.55 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.85 (0.30), residues: 769 helix: -5.44 (0.46), residues: 6 sheet: -0.21 (0.34), residues: 234 loop : -0.66 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 PHE 0.009 0.001 PHEA1 535 TYR 0.010 0.001 TYRA1 510 ARG 0.008 0.000 ARGH2 84 =============================================================================== Job complete usr+sys time: 3130.95 seconds wall clock time: 54 minutes 38.73 seconds (3278.73 seconds total)