Starting phenix.real_space_refine on Fri Dec 8 00:20:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_23656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_23656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_23656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_23656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3l_23656/12_2023/7m3l_23656.pdb" } 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 Residue "A1 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 60": "OE1" <-> "OE2" Residue "A1 ARG 67": "NH1" <-> "NH2" Residue "A1 GLU 77": "OE1" <-> "OE2" Residue "A1 ASP 88": "OD1" <-> "OD2" Residue "A1 ASP 113": "OD1" <-> "OD2" Residue "A1 GLU 155": "OE1" <-> "OE2" Residue "A1 ASP 168": "OD1" <-> "OD2" Residue "A1 GLU 193": "OE1" <-> "OE2" Residue "A1 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 259": "OD1" <-> "OD2" Residue "A1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 269": "OD1" <-> "OD2" Residue "A1 GLU 346": "OE1" <-> "OE2" Residue "A1 ASP 367": "OD1" <-> "OD2" Residue "A1 ASP 373": "OD1" <-> "OD2" Residue "A1 TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 393": "OE1" <-> "OE2" Residue "A1 GLU 396": "OE1" <-> "OE2" Residue "A1 PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 405": "OD1" <-> "OD2" Residue "A1 GLU 411": "OE1" <-> "OE2" Residue "A1 ASP 434": "OD1" <-> "OD2" Residue "A1 TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 473": "OE1" <-> "OE2" Residue "A1 ASP 511": "OD1" <-> "OD2" Residue "A1 PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 556": "OD1" <-> "OD2" Residue "A1 TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 ASP 28": "OD1" <-> "OD2" Residue "L2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 ASP 60": "OD1" <-> "OD2" Residue "L2 ARG 61": "NH1" <-> "NH2" Residue "L2 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 GLU 81": "OE1" <-> "OE2" Residue "L2 ASP 82": "OD1" <-> "OD2" Residue "L2 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 GLU 8": "OE1" <-> "OE2" Residue "H2 GLU 42": "OE1" <-> "OE2" Residue "H2 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 ASP 73": "OD1" <-> "OD2" Residue "H2 TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.80, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.70 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: 1.69 Time building geometry restraints manager: 2.28 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: 98.82 - 106.58: 244 106.58 - 114.34: 3481 114.34 - 122.10: 3436 122.10 - 129.86: 1361 129.86 - 137.62: 57 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 2.520 nonbonded pdb=" OD2 ASPH2 33 " pdb=" OH TYRH2 104 " model vdw 2.297 2.440 nonbonded pdb=" OG SERL2 43 " pdb=" O GLYH2 110 " model vdw 2.307 2.440 ... (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 ========== 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: 3.270 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: 12.740 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.420 Find NCS groups from input model: 0.170 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.759 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: 0.2604 time to fit residues: 25.2635 Evaluate side-chains 39 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9661 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 38 optimal weight: 0.0000 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- 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 222 HIS 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 550 GLN L2 37 GLN L2 38 GLN L2 53 ASN ** L2 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 39 GLN H2 43 GLN H2 101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4308 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6286 Z= 0.217 Angle : 0.636 10.342 8579 Z= 0.328 Chirality : 0.044 0.146 923 Planarity : 0.006 0.065 1122 Dihedral : 6.139 58.075 839 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 3.16 % Allowed : 15.04 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.14 % 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: -2.34 (0.27), residues: 769 helix: -4.63 (0.62), residues: 12 sheet: -1.34 (0.31), residues: 234 loop : -1.64 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPH2 50 HIS 0.005 0.001 HISH2 101 PHE 0.018 0.002 PHEA1 527 TYR 0.011 0.001 TYRL2 92 ARG 0.004 0.001 ARGH2 84 *********************** 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 70 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 68 average time/residue: 0.2126 time to fit residues: 18.9348 Evaluate side-chains 47 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0869 time to fit residues: 2.2181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 60 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 131 ASN A1 143 GLN A1 181 ASN ** A1 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 38 GLN H2 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6286 Z= 0.286 Angle : 0.702 11.878 8579 Z= 0.357 Chirality : 0.045 0.228 923 Planarity : 0.006 0.054 1122 Dihedral : 5.937 48.675 839 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.41 % Favored : 92.33 % Rotamer: Outliers : 3.46 % Allowed : 16.09 % Favored : 80.45 % 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: -1.82 (0.29), residues: 769 helix: -4.08 (1.08), residues: 12 sheet: -0.93 (0.32), residues: 238 loop : -1.31 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPH2 50 HIS 0.004 0.001 HISL2 91 PHE 0.022 0.002 PHEH2 64 TYR 0.010 0.001 TYRA1 510 ARG 0.012 0.001 ARGH2 59 *********************** 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 58 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 35 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 56 average time/residue: 0.2459 time to fit residues: 17.8901 Evaluate side-chains 34 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0661 time to fit residues: 1.9963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 0.0270 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 overall best weight: 5.5844 ------------------------------------------------------------------------------- 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 296 GLN A1 483 HIS L2 6 GLN H2 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 0.8305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6286 Z= 0.230 Angle : 0.603 8.538 8579 Z= 0.307 Chirality : 0.042 0.144 923 Planarity : 0.004 0.052 1122 Dihedral : 5.475 49.455 839 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 1.95 % Allowed : 17.59 % Favored : 80.45 % 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: -1.47 (0.29), residues: 769 helix: -4.01 (1.15), residues: 12 sheet: -0.72 (0.32), residues: 225 loop : -1.04 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPH2 50 HIS 0.002 0.001 HISA1 234 PHE 0.013 0.001 PHEA1 266 TYR 0.011 0.001 TYRA1 510 ARG 0.008 0.001 ARGH2 84 *********************** 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 45 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 44 average time/residue: 0.2580 time to fit residues: 14.8880 Evaluate side-chains 28 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0763 time to fit residues: 1.3740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 30.0000 chunk 50 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 overall best weight: 2.7204 ------------------------------------------------------------------------------- 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 384 HIS A1 560 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6286 Z= 0.157 Angle : 0.567 8.145 8579 Z= 0.281 Chirality : 0.042 0.154 923 Planarity : 0.004 0.051 1122 Dihedral : 5.125 47.327 839 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 1.05 % Allowed : 18.80 % Favored : 80.15 % 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: -1.23 (0.29), residues: 769 helix: -4.12 (1.07), residues: 12 sheet: -0.58 (0.32), residues: 240 loop : -0.85 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPH2 50 HIS 0.003 0.001 HISL2 8 PHE 0.009 0.001 PHEA1 420 TYR 0.006 0.001 TYRA1 510 ARG 0.006 0.000 ARGL2 18 *********************** 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 39 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.2692 time to fit residues: 12.6965 Evaluate side-chains 29 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0630 time to fit residues: 1.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- 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** H2 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.9584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6286 Z= 0.174 Angle : 0.562 7.723 8579 Z= 0.279 Chirality : 0.041 0.139 923 Planarity : 0.004 0.047 1122 Dihedral : 4.946 45.875 839 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 0.90 % Allowed : 19.10 % Favored : 80.00 % 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: -1.08 (0.30), residues: 769 helix: -4.15 (1.05), residues: 12 sheet: -0.45 (0.33), residues: 231 loop : -0.75 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPH2 50 HIS 0.003 0.001 HISL2 8 PHE 0.019 0.001 PHEL2 10 TYR 0.007 0.001 TYRA1 510 ARG 0.006 0.000 ARGL2 18 *********************** 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 37 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.2388 time to fit residues: 11.6506 Evaluate side-chains 28 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0605 time to fit residues: 1.1567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 0.0370 chunk 43 optimal weight: 5.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 147 ASN ** L2 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5230 moved from start: 1.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6286 Z= 0.182 Angle : 0.596 14.880 8579 Z= 0.285 Chirality : 0.042 0.146 923 Planarity : 0.004 0.054 1122 Dihedral : 4.958 43.568 839 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 0.45 % Allowed : 19.85 % 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: -0.90 (0.30), residues: 769 helix: -5.42 (0.47), residues: 6 sheet: -0.06 (0.35), residues: 218 loop : -0.79 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPH2 50 HIS 0.003 0.001 HISA1 137 PHE 0.011 0.001 PHEL2 10 TYR 0.011 0.001 TYRL2 86 ARG 0.005 0.000 ARGA1 332 *********************** 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 32 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.2724 time to fit residues: 11.3465 Evaluate side-chains 31 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0749 time to fit residues: 1.1731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 40.0000 chunk 56 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 181 ASN ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 moved from start: 1.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6286 Z= 0.179 Angle : 0.568 9.034 8579 Z= 0.279 Chirality : 0.041 0.139 923 Planarity : 0.004 0.043 1122 Dihedral : 4.818 43.147 839 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 0.45 % Allowed : 20.90 % Favored : 78.65 % 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: -0.75 (0.30), residues: 769 helix: -5.40 (0.49), residues: 6 sheet: 0.09 (0.35), residues: 218 loop : -0.70 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPH2 50 HIS 0.002 0.001 HISH2 101 PHE 0.009 0.001 PHEA1 535 TYR 0.007 0.001 TYRA1 510 ARG 0.005 0.000 ARGL2 18 *********************** 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 34 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.2636 time to fit residues: 11.9382 Evaluate side-chains 29 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 43 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: ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 1.2194 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= 0.230 Angle : 0.615 11.942 8579 Z= 0.300 Chirality : 0.042 0.147 923 Planarity : 0.004 0.043 1122 Dihedral : 5.052 43.380 839 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.50 % Favored : 93.37 % Rotamer: Outliers : 0.75 % Allowed : 20.75 % Favored : 78.50 % 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: -0.65 (0.31), residues: 769 helix: -5.42 (0.47), residues: 6 sheet: 0.16 (0.35), residues: 228 loop : -0.65 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPH2 50 HIS 0.003 0.001 HISH2 3 PHE 0.008 0.001 PHEA1 535 TYR 0.017 0.001 TYRA1 510 ARG 0.006 0.001 ARGA1 332 *********************** 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 35 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.2518 time to fit residues: 10.8361 Evaluate side-chains 32 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0571 time to fit residues: 1.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 40.0000 chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 18 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: ** H2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 1.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6286 Z= 0.236 Angle : 0.617 9.765 8579 Z= 0.306 Chirality : 0.042 0.146 923 Planarity : 0.004 0.043 1122 Dihedral : 5.178 44.269 839 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 21.50 % Favored : 78.50 % 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: -0.68 (0.31), residues: 769 helix: -5.41 (0.48), residues: 6 sheet: 0.12 (0.35), residues: 228 loop : -0.65 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPH2 50 HIS 0.002 0.001 HISH2 3 PHE 0.007 0.001 PHEA1 267 TYR 0.015 0.001 TYRA1 510 ARG 0.003 0.000 ARGA1 191 ********************** 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 31 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2335 time to fit residues: 9.9867 Evaluate side-chains 29 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 59 optimal weight: 40.0000 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 39 GLN ** 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 = 0.3672 r_free = 0.3672 target = 0.047462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.040685 restraints weight = 67798.808| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 7.39 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 1.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6286 Z= 0.208 Angle : 0.601 10.794 8579 Z= 0.294 Chirality : 0.042 0.147 923 Planarity : 0.004 0.043 1122 Dihedral : 5.107 44.126 839 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 0.30 % Allowed : 21.50 % Favored : 78.20 % 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: -0.73 (0.31), residues: 769 helix: -5.42 (0.48), residues: 6 sheet: 0.08 (0.35), residues: 230 loop : -0.69 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPH2 50 HIS 0.002 0.001 HISA1 222 PHE 0.007 0.001 PHEA1 535 TYR 0.014 0.001 TYRA1 510 ARG 0.003 0.000 ARGA1 191 =============================================================================== Job complete usr+sys time: 1474.56 seconds wall clock time: 27 minutes 36.55 seconds (1656.55 seconds total)