Starting phenix.real_space_refine on Tue Mar 3 14:23:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_23656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_23656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_23656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_23656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3l_23656/03_2026/7m3l_23656.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.47, per 1000 atoms: 0.24 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: 0.34 Conformation dependent library (CDL) restraints added in 482.1 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: 0.19 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: 0.73 Time building geometry restraints manager: 0.48 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- 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 6288 Z= 0.385 Angle : 0.967 16.208 8583 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 : 6.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (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 ARG 0.006 0.001 ARGH2 84 TYR 0.030 0.003 TYRA1 342 PHE 0.020 0.003 PHEA1 45 TRP 0.053 0.003 TRPH2 50 HIS 0.009 0.002 HISA1 403 Details of bonding type rmsd covalent geometry : bond 0.00903 ( 6286) covalent geometry : angle 0.96622 ( 8579) SS BOND : bond 0.00779 ( 2) SS BOND : angle 1.50850 ( 4) hydrogen bonds : bond 0.25357 ( 121) hydrogen bonds : angle 11.13522 ( 288) *********************** 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 : 0.243 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: 0.1104 time to fit residues: 10.8202 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 6.9990 overall best weight: 4.4224 ------------------------------------------------------------------------------- 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 234 HIS A1 242 GLN ** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 403 HIS A1 416 GLN A1 419 ASN A1 466 ASN A1 468 GLN A1 483 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.057605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.050240 restraints weight = 57994.749| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 7.55 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6288 Z= 0.160 Angle : 0.657 8.977 8583 Z= 0.337 Chirality : 0.044 0.140 923 Planarity : 0.006 0.064 1122 Dihedral : 6.374 63.541 839 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.11 % Allowed : 14.74 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.27), residues: 769 helix: -4.53 (0.70), residues: 12 sheet: -1.41 (0.31), residues: 244 loop : -1.57 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGA1 80 TYR 0.015 0.001 TYRL2 92 PHE 0.016 0.002 PHEA1 527 TRP 0.021 0.001 TRPH2 50 HIS 0.004 0.001 HISH2 101 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6286) covalent geometry : angle 0.65668 ( 8579) SS BOND : bond 0.00752 ( 2) SS BOND : angle 1.22967 ( 4) hydrogen bonds : bond 0.03729 ( 121) hydrogen bonds : angle 7.00221 ( 288) *********************** 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 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A1 60 GLU cc_start: 0.8580 (tp30) cc_final: 0.8374 (tp30) REVERT: L2 4 MET cc_start: 0.6451 (mmm) cc_final: 0.4024 (tpp) REVERT: L2 24 LYS cc_start: 0.9285 (mmtm) cc_final: 0.9041 (mmmt) REVERT: H2 65 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9353 (mmmt) REVERT: H2 74 LYS cc_start: 0.9288 (mmtp) cc_final: 0.8968 (mptt) outliers start: 14 outliers final: 7 residues processed: 60 average time/residue: 0.1177 time to fit residues: 8.8971 Evaluate side-chains 42 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 482 LEU 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 14 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 47 ASN A1 85 ASN A1 102 HIS A1 143 GLN A1 181 ASN ** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 384 HIS A1 550 GLN ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.050366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043719 restraints weight = 72363.561| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 7.19 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.9609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 6288 Z= 0.278 Angle : 0.881 14.223 8583 Z= 0.455 Chirality : 0.049 0.193 923 Planarity : 0.007 0.074 1122 Dihedral : 7.050 56.099 839 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 4.21 % Allowed : 14.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.28), residues: 769 helix: -4.27 (0.92), residues: 12 sheet: -1.06 (0.32), residues: 235 loop : -1.52 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGH2 84 TYR 0.020 0.002 TYRA1 510 PHE 0.019 0.002 PHEA1 266 TRP 0.016 0.002 TRPH2 36 HIS 0.009 0.002 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 6286) covalent geometry : angle 0.88039 ( 8579) SS BOND : bond 0.00446 ( 2) SS BOND : angle 1.24331 ( 4) hydrogen bonds : bond 0.04802 ( 121) hydrogen bonds : angle 7.18288 ( 288) *********************** 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 67 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 137 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (p90) REVERT: L2 4 MET cc_start: 0.8993 (mmm) cc_final: 0.8637 (tpp) REVERT: H2 46 GLU cc_start: 0.8731 (tp30) cc_final: 0.8433 (tm-30) REVERT: H2 74 LYS cc_start: 0.9712 (mmtp) cc_final: 0.9480 (mmtm) outliers start: 28 outliers final: 11 residues processed: 65 average time/residue: 0.1067 time to fit residues: 8.8566 Evaluate side-chains 41 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 137 HIS 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 403 HIS Chi-restraints excluded: chain A1 residue 554 ASN Chi-restraints excluded: chain L2 residue 5 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 560 ASN ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.048964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.042016 restraints weight = 66365.177| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 7.31 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 1.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6288 Z= 0.189 Angle : 0.652 9.793 8583 Z= 0.330 Chirality : 0.043 0.157 923 Planarity : 0.005 0.057 1122 Dihedral : 6.030 58.659 839 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 2.71 % Allowed : 15.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.29), residues: 769 helix: -4.13 (1.05), residues: 12 sheet: -0.74 (0.33), residues: 229 loop : -1.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGH2 84 TYR 0.013 0.001 TYRA1 510 PHE 0.010 0.001 PHEA1 535 TRP 0.025 0.002 TRPH2 50 HIS 0.004 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6286) covalent geometry : angle 0.65157 ( 8579) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.69446 ( 4) hydrogen bonds : bond 0.03205 ( 121) hydrogen bonds : angle 5.98902 ( 288) *********************** 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 52 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H2 46 GLU cc_start: 0.9062 (tp30) cc_final: 0.8559 (tm-30) outliers start: 18 outliers final: 9 residues processed: 51 average time/residue: 0.0955 time to fit residues: 6.4585 Evaluate side-chains 39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 54 LEU Chi-restraints excluded: chain A1 residue 96 MET 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 L2 residue 5 THR Chi-restraints excluded: chain H2 residue 2 VAL Chi-restraints excluded: chain H2 residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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** L2 38 GLN H2 5 GLN H2 39 GLN H2 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.048879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.041884 restraints weight = 68498.870| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 7.70 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 1.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6288 Z= 0.104 Angle : 0.599 9.198 8583 Z= 0.297 Chirality : 0.043 0.164 923 Planarity : 0.004 0.062 1122 Dihedral : 5.442 56.753 839 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 1.80 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.29), residues: 769 helix: -4.17 (1.03), residues: 12 sheet: -0.68 (0.33), residues: 223 loop : -0.95 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGL2 18 TYR 0.007 0.001 TYRA1 510 PHE 0.011 0.001 PHEA1 535 TRP 0.022 0.001 TRPH2 50 HIS 0.003 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6286) covalent geometry : angle 0.59921 ( 8579) SS BOND : bond 0.00923 ( 2) SS BOND : angle 0.92574 ( 4) hydrogen bonds : bond 0.02863 ( 121) hydrogen bonds : angle 5.30350 ( 288) *********************** 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 50 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.8834 (mmm) cc_final: 0.8380 (mmp) REVERT: A1 183 MET cc_start: 0.9349 (mmm) cc_final: 0.9054 (mmm) REVERT: L2 4 MET cc_start: 0.9129 (tpp) cc_final: 0.8854 (tpp) REVERT: H2 46 GLU cc_start: 0.9028 (tp30) cc_final: 0.8788 (tm-30) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.0974 time to fit residues: 5.9281 Evaluate side-chains 40 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 96 MET Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 43 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** L2 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.048606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.041778 restraints weight = 66978.445| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 7.26 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 1.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6288 Z= 0.116 Angle : 0.603 11.195 8583 Z= 0.296 Chirality : 0.042 0.140 923 Planarity : 0.004 0.050 1122 Dihedral : 5.237 55.470 839 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 1.50 % Allowed : 17.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.30), residues: 769 helix: -4.15 (1.05), residues: 12 sheet: -0.79 (0.32), residues: 239 loop : -0.78 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGL2 18 TYR 0.007 0.001 TYRA1 510 PHE 0.009 0.001 PHEA1 535 TRP 0.020 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6286) covalent geometry : angle 0.60293 ( 8579) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.83514 ( 4) hydrogen bonds : bond 0.02643 ( 121) hydrogen bonds : angle 5.01393 ( 288) *********************** 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 44 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.9024 (mmm) cc_final: 0.8545 (mmp) REVERT: L2 4 MET cc_start: 0.9256 (tpp) cc_final: 0.9016 (tpp) REVERT: L2 17 ASP cc_start: 0.9414 (m-30) cc_final: 0.9195 (p0) REVERT: L2 70 ASP cc_start: 0.9792 (p0) cc_final: 0.9532 (t0) REVERT: H2 34 MET cc_start: 0.8571 (tpp) cc_final: 0.8291 (tpp) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.0989 time to fit residues: 5.5055 Evaluate side-chains 38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 0.0010 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 38 optimal weight: 0.0030 chunk 67 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 overall best weight: 2.2178 ------------------------------------------------------------------------------- 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** H2 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.048495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.041498 restraints weight = 63543.634| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 7.06 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6288 Z= 0.101 Angle : 0.580 10.097 8583 Z= 0.285 Chirality : 0.042 0.139 923 Planarity : 0.004 0.051 1122 Dihedral : 4.975 54.107 839 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 1.20 % Allowed : 17.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 769 helix: -5.43 (0.47), residues: 6 sheet: -0.73 (0.32), residues: 239 loop : -0.68 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGL2 18 TYR 0.005 0.001 TYRA1 342 PHE 0.009 0.001 PHEA1 535 TRP 0.018 0.001 TRPH2 50 HIS 0.003 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6286) covalent geometry : angle 0.57998 ( 8579) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.73237 ( 4) hydrogen bonds : bond 0.02528 ( 121) hydrogen bonds : angle 4.67974 ( 288) *********************** 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 42 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.9065 (mmm) cc_final: 0.8604 (mmp) REVERT: A1 183 MET cc_start: 0.9362 (mmm) cc_final: 0.9012 (mmm) REVERT: A1 319 MET cc_start: 0.6945 (mmm) cc_final: 0.6704 (tpt) REVERT: L2 70 ASP cc_start: 0.9792 (p0) cc_final: 0.9543 (t0) REVERT: H2 34 MET cc_start: 0.8606 (tpp) cc_final: 0.8325 (tpp) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.1137 time to fit residues: 5.8313 Evaluate side-chains 38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain H2 residue 43 GLN Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 45 optimal weight: 0.0770 overall best weight: 1.7544 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.048656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.041511 restraints weight = 64215.797| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 7.33 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 1.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6288 Z= 0.096 Angle : 0.581 9.776 8583 Z= 0.284 Chirality : 0.042 0.138 923 Planarity : 0.004 0.049 1122 Dihedral : 4.833 52.597 839 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 1.35 % Allowed : 18.20 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.30), residues: 769 helix: -5.42 (0.48), residues: 6 sheet: -0.52 (0.33), residues: 224 loop : -0.65 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGL2 18 TYR 0.005 0.001 TYRL2 49 PHE 0.008 0.001 PHEA1 535 TRP 0.018 0.001 TRPH2 50 HIS 0.003 0.000 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6286) covalent geometry : angle 0.58069 ( 8579) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.71440 ( 4) hydrogen bonds : bond 0.02471 ( 121) hydrogen bonds : angle 4.64700 ( 288) *********************** 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 44 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.9083 (mmm) cc_final: 0.8632 (mmp) REVERT: H2 34 MET cc_start: 0.8573 (tpp) cc_final: 0.8311 (tpp) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1130 time to fit residues: 6.5133 Evaluate side-chains 39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 324 TYR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 17 ASP Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.047398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.040845 restraints weight = 68595.027| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 6.96 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 1.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6288 Z= 0.159 Angle : 0.633 10.777 8583 Z= 0.312 Chirality : 0.043 0.157 923 Planarity : 0.004 0.049 1122 Dihedral : 5.154 52.090 839 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 1.65 % Allowed : 18.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.30), residues: 769 helix: -5.45 (0.45), residues: 6 sheet: -0.20 (0.34), residues: 230 loop : -0.69 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGH2 84 TYR 0.014 0.001 TYRA1 510 PHE 0.009 0.001 PHEL2 71 TRP 0.017 0.001 TRPH2 50 HIS 0.005 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6286) covalent geometry : angle 0.63358 ( 8579) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.28065 ( 4) hydrogen bonds : bond 0.02860 ( 121) hydrogen bonds : angle 4.74855 ( 288) *********************** 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 47 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.9171 (mmm) cc_final: 0.8957 (mmm) REVERT: A1 518 MET cc_start: 0.8462 (tpp) cc_final: 0.8108 (tpp) REVERT: H2 34 MET cc_start: 0.8592 (tpp) cc_final: 0.8336 (tpp) REVERT: H2 46 GLU cc_start: 0.9358 (tp30) cc_final: 0.8971 (tm-30) REVERT: H2 74 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9150 (mmmt) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.1047 time to fit residues: 6.1281 Evaluate side-chains 42 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 132 THR Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 482 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain L2 residue 17 ASP Chi-restraints excluded: chain L2 residue 47 LEU Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.047184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.040221 restraints weight = 63017.989| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 6.88 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 1.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6288 Z= 0.137 Angle : 0.617 10.882 8583 Z= 0.305 Chirality : 0.042 0.141 923 Planarity : 0.004 0.048 1122 Dihedral : 5.030 52.732 839 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 1.20 % Allowed : 18.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.30), residues: 769 helix: -5.45 (0.45), residues: 6 sheet: -0.29 (0.34), residues: 234 loop : -0.64 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGH2 84 TYR 0.009 0.001 TYRA1 510 PHE 0.011 0.001 PHEA1 535 TRP 0.017 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6286) covalent geometry : angle 0.61695 ( 8579) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.61873 ( 4) hydrogen bonds : bond 0.02764 ( 121) hydrogen bonds : angle 4.73437 ( 288) ********************** 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 41 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 87 MET cc_start: 0.9100 (mmm) cc_final: 0.8887 (mmm) REVERT: L2 70 ASP cc_start: 0.9830 (p0) cc_final: 0.9593 (t0) REVERT: H2 34 MET cc_start: 0.8555 (tpp) cc_final: 0.8279 (tpp) REVERT: H2 46 GLU cc_start: 0.9452 (tp30) cc_final: 0.9027 (tm-30) outliers start: 8 outliers final: 8 residues processed: 40 average time/residue: 0.1014 time to fit residues: 5.4217 Evaluate side-chains 39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 336 VAL Chi-restraints excluded: chain A1 residue 482 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 8 HIS Chi-restraints excluded: chain L2 residue 17 ASP Chi-restraints excluded: chain L2 residue 47 LEU Chi-restraints excluded: chain H2 residue 18 VAL Chi-restraints excluded: chain H2 residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L2 27 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 = 0.3649 r_free = 0.3649 target = 0.046738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.040035 restraints weight = 67366.804| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 6.82 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 1.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6288 Z= 0.155 Angle : 0.646 12.325 8583 Z= 0.320 Chirality : 0.042 0.136 923 Planarity : 0.004 0.049 1122 Dihedral : 5.134 52.070 839 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.30), residues: 769 helix: -5.46 (0.44), residues: 6 sheet: -0.21 (0.34), residues: 235 loop : -0.65 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGH2 84 TYR 0.012 0.001 TYRA1 510 PHE 0.009 0.001 PHEA1 535 TRP 0.016 0.001 TRPH2 50 HIS 0.004 0.001 HISA1 222 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6286) covalent geometry : angle 0.64632 ( 8579) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.37253 ( 4) hydrogen bonds : bond 0.02708 ( 121) hydrogen bonds : angle 4.72894 ( 288) =============================================================================== Job complete usr+sys time: 1794.16 seconds wall clock time: 31 minutes 29.53 seconds (1889.53 seconds total)