Starting phenix.real_space_refine on Fri Dec 8 05:50:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/12_2023/8tzb_41753_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4632 2.51 5 N 1274 2.21 5 O 1335 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1745": "OE1" <-> "OE2" Residue "A GLU 1821": "OE1" <-> "OE2" Residue "A TYR 1894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2277": "OD1" <-> "OD2" Residue "A GLU 2337": "OE1" <-> "OE2" Residue "A ASP 2377": "OD1" <-> "OD2" Residue "A GLU 2381": "OE1" <-> "OE2" Residue "A ASP 2438": "OD1" <-> "OD2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 6752 Classifications: {'peptide': 920} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 42, 'TRANS': 877} Chain breaks: 33 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 492 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.41, per 1000 atoms: 0.61 Number of scatterers: 7283 At special positions: 0 Unit cell: (74.8, 94.435, 145.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 F 3 9.00 O 1335 8.00 N 1274 7.00 C 4632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2452 " - pdb=" SG CYS A2492 " distance=2.04 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 13 sheets defined 28.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 1347 through 1351 Processing helix chain 'A' and resid 1430 through 1434 removed outlier: 3.685A pdb=" N TRP A1434 " --> pdb=" O ALA A1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1430 through 1434' Processing helix chain 'A' and resid 1460 through 1470 removed outlier: 3.940A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1509 Processing helix chain 'A' and resid 1529 through 1538 removed outlier: 4.125A pdb=" N SER A1536 " --> pdb=" O LYS A1532 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A1537 " --> pdb=" O ILE A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1557 removed outlier: 3.890A pdb=" N VAL A1557 " --> pdb=" O LEU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1564 Processing helix chain 'A' and resid 1606 through 1611 removed outlier: 3.666A pdb=" N ILE A1610 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU A1611 " --> pdb=" O MET A1607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1606 through 1611' Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1704 through 1711 Processing helix chain 'A' and resid 1773 through 1790 Processing helix chain 'A' and resid 1827 through 1836 Processing helix chain 'A' and resid 1852 through 1854 No H-bonds generated for 'chain 'A' and resid 1852 through 1854' Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1914 through 1926 removed outlier: 4.192A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1960 Processing helix chain 'A' and resid 1968 through 1987 Processing helix chain 'A' and resid 1997 through 1999 No H-bonds generated for 'chain 'A' and resid 1997 through 1999' Processing helix chain 'A' and resid 2052 through 2067 Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2095 through 2098 No H-bonds generated for 'chain 'A' and resid 2095 through 2098' Processing helix chain 'A' and resid 2108 through 2114 Processing helix chain 'A' and resid 2125 through 2132 Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 4.194A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2135 through 2139' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2338 through 2340 No H-bonds generated for 'chain 'A' and resid 2338 through 2340' Processing helix chain 'A' and resid 2347 through 2350 No H-bonds generated for 'chain 'A' and resid 2347 through 2350' Processing helix chain 'A' and resid 2389 through 2395 Processing helix chain 'A' and resid 2498 through 2521 Proline residue: A2501 - end of helix removed outlier: 4.433A pdb=" N VAL A2504 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A2507 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A2511 " --> pdb=" O GLU A2508 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 128 through 137 Processing sheet with id= A, first strand: chain 'A' and resid 1447 through 1450 removed outlier: 7.441A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1340 " --> pdb=" O VAL A1418 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1823 through 1826 removed outlier: 4.436A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1839 through 1841 Processing sheet with id= D, first strand: chain 'A' and resid 1893 through 1897 Processing sheet with id= E, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id= F, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 6.708A pdb=" N GLY A2170 " --> pdb=" O GLU A2153 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET A2155 " --> pdb=" O TRP A2168 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2168 " --> pdb=" O MET A2155 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA A2157 " --> pdb=" O SER A2166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER A2166 " --> pdb=" O ALA A2157 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A2178 " --> pdb=" O CYS A2171 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A2179 " --> pdb=" O GLU A2193 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU A2193 " --> pdb=" O LEU A2179 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A2181 " --> pdb=" O SER A2191 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER A2191 " --> pdb=" O PHE A2181 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2235 through 2237 Processing sheet with id= H, first strand: chain 'A' and resid 2273 through 2275 Processing sheet with id= I, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 6.425A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2373 through 2377 Processing sheet with id= K, first strand: chain 'A' and resid 2434 through 2437 Processing sheet with id= L, first strand: chain 'A' and resid 2457 through 2461 removed outlier: 6.619A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1739 through 1743 removed outlier: 6.504A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 672 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: 2.67 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1235 1.30 - 1.43: 1730 1.43 - 1.56: 4352 1.56 - 1.68: 1 1.68 - 1.81: 59 Bond restraints: 7377 Sorted by residual: bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.300 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.453 1.305 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.313 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.453 1.314 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C20 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.452 1.320 0.132 2.00e-02 2.50e+03 4.32e+01 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 96.05 - 112.73: 4236 112.73 - 129.41: 5721 129.41 - 146.08: 53 146.08 - 162.76: 0 162.76 - 179.44: 2 Bond angle restraints: 10012 Sorted by residual: angle pdb=" C33 T3X A2601 " pdb=" C37 T3X A2601 " pdb=" N36 T3X A2601 " ideal model delta sigma weight residual 108.00 122.27 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C34 T3X A2601 " pdb=" N35 T3X A2601 " pdb=" N36 T3X A2601 " ideal model delta sigma weight residual 108.04 121.84 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C37 T3X A2601 " pdb=" N36 T3X A2601 " pdb=" N35 T3X A2601 " ideal model delta sigma weight residual 108.06 96.05 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N VAL A2194 " pdb=" CA VAL A2194 " pdb=" C VAL A2194 " ideal model delta sigma weight residual 113.71 110.63 3.08 9.50e-01 1.11e+00 1.05e+01 angle pdb=" CA TYR A2018 " pdb=" C TYR A2018 " pdb=" O TYR A2018 " ideal model delta sigma weight residual 122.38 117.65 4.73 1.49e+00 4.50e-01 1.01e+01 ... (remaining 10007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3990 17.72 - 35.44: 327 35.44 - 53.16: 69 53.16 - 70.88: 17 70.88 - 88.60: 10 Dihedral angle restraints: 4413 sinusoidal: 1494 harmonic: 2919 Sorted by residual: dihedral pdb=" CA VAL A2359 " pdb=" C VAL A2359 " pdb=" N ASP A2360 " pdb=" CA ASP A2360 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CB CYS A2452 " pdb=" SG CYS A2452 " pdb=" SG CYS A2492 " pdb=" CB CYS A2492 " ideal model delta sinusoidal sigma weight residual -86.00 -55.70 -30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" C19 T3X A2601 " pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " pdb=" C22 T3X A2601 " ideal model delta sinusoidal sigma weight residual 52.94 -35.66 88.60 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 867 0.042 - 0.083: 262 0.083 - 0.124: 79 0.124 - 0.166: 9 0.166 - 0.207: 1 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CB ILE A2365 " pdb=" CA ILE A2365 " pdb=" CG1 ILE A2365 " pdb=" CG2 ILE A2365 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU B 86 " pdb=" N LEU B 86 " pdb=" C LEU B 86 " pdb=" CB LEU B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE A2336 " pdb=" N ILE A2336 " pdb=" C ILE A2336 " pdb=" CB ILE A2336 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1215 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1880 " 0.062 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO A1881 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A1881 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1881 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2207 " -0.052 5.00e-02 4.00e+02 7.90e-02 1.00e+01 pdb=" N PRO A2208 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A2208 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A2208 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A1942 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.042 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 298 2.72 - 3.27: 7068 3.27 - 3.81: 11454 3.81 - 4.36: 13707 4.36 - 4.90: 23399 Nonbonded interactions: 55926 Sorted by model distance: nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR A1992 " pdb=" ND2 ASN A1999 " model vdw 2.185 2.520 nonbonded pdb=" OH TYR A2249 " pdb=" OE1 GLU A2305 " model vdw 2.252 2.440 nonbonded pdb=" NE1 TRP A2104 " pdb=" O LEU A2137 " model vdw 2.256 2.520 nonbonded pdb=" N ARG A2456 " pdb=" O LEU A2473 " model vdw 2.272 2.520 ... (remaining 55921 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.030 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.210 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.006 0.153 7377 Z= 0.395 Angle : 0.651 14.274 10012 Z= 0.328 Chirality : 0.043 0.207 1218 Planarity : 0.005 0.092 1263 Dihedral : 15.014 88.598 2490 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 0.30 % Allowed : 17.72 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.28), residues: 940 helix: 0.92 (0.33), residues: 279 sheet: -0.64 (0.34), residues: 213 loop : -0.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2496 HIS 0.009 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.019 0.001 TYR A1739 ARG 0.006 0.001 ARG A2446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.847 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.2180 time to fit residues: 24.9462 Evaluate side-chains 83 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0670 time to fit residues: 1.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7377 Z= 0.237 Angle : 0.529 7.122 10012 Z= 0.266 Chirality : 0.042 0.145 1218 Planarity : 0.005 0.064 1263 Dihedral : 6.759 90.425 1042 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.53 % Favored : 94.36 % Rotamer: Outliers : 2.10 % Allowed : 18.17 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.28), residues: 940 helix: 0.87 (0.33), residues: 285 sheet: -0.66 (0.34), residues: 212 loop : -0.75 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.017 0.001 TYR A1739 ARG 0.004 0.000 ARG A2446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.853 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 0.1918 time to fit residues: 25.6002 Evaluate side-chains 89 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0696 time to fit residues: 1.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7377 Z= 0.342 Angle : 0.603 8.274 10012 Z= 0.302 Chirality : 0.044 0.159 1218 Planarity : 0.005 0.065 1263 Dihedral : 6.964 91.117 1042 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.38 % Favored : 93.51 % Rotamer: Outliers : 3.75 % Allowed : 17.42 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 940 helix: 0.64 (0.32), residues: 280 sheet: -0.89 (0.34), residues: 211 loop : -0.92 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1811 HIS 0.007 0.001 HIS A1998 PHE 0.016 0.002 PHE A2059 TYR 0.023 0.002 TYR A1739 ARG 0.003 0.001 ARG A1711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.561 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 111 average time/residue: 0.2076 time to fit residues: 31.9257 Evaluate side-chains 98 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1395 time to fit residues: 3.5753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7377 Z= 0.349 Angle : 0.612 7.216 10012 Z= 0.306 Chirality : 0.044 0.159 1218 Planarity : 0.005 0.061 1263 Dihedral : 7.051 92.818 1042 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 2.85 % Allowed : 19.37 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 940 helix: 0.44 (0.32), residues: 281 sheet: -1.01 (0.33), residues: 211 loop : -1.03 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2426 HIS 0.006 0.001 HIS A1998 PHE 0.015 0.002 PHE A2059 TYR 0.017 0.002 TYR A1739 ARG 0.004 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.831 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 0.2194 time to fit residues: 31.8873 Evaluate side-chains 93 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0870 time to fit residues: 2.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1657 GLN A2505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7377 Z= 0.154 Angle : 0.505 8.129 10012 Z= 0.254 Chirality : 0.042 0.141 1218 Planarity : 0.004 0.057 1263 Dihedral : 6.750 89.525 1042 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.53 % Favored : 94.36 % Rotamer: Outliers : 1.65 % Allowed : 19.82 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 940 helix: 0.90 (0.33), residues: 285 sheet: -0.72 (0.34), residues: 216 loop : -0.77 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2426 HIS 0.005 0.001 HIS A2391 PHE 0.019 0.001 PHE A1792 TYR 0.010 0.001 TYR A2018 ARG 0.006 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.864 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 0.2107 time to fit residues: 27.3970 Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0701 time to fit residues: 1.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0670 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7377 Z= 0.176 Angle : 0.512 6.858 10012 Z= 0.258 Chirality : 0.042 0.141 1218 Planarity : 0.004 0.054 1263 Dihedral : 6.725 91.311 1042 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.65 % Allowed : 19.82 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.28), residues: 940 helix: 0.99 (0.33), residues: 285 sheet: -0.64 (0.33), residues: 218 loop : -0.79 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2426 HIS 0.008 0.001 HIS A2391 PHE 0.013 0.001 PHE A2059 TYR 0.009 0.001 TYR A2018 ARG 0.006 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.876 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 99 average time/residue: 0.1753 time to fit residues: 25.1914 Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1615 time to fit residues: 1.8313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0030 chunk 55 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 97 optimal weight: 0.0970 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 overall best weight: 0.0746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7377 Z= 0.112 Angle : 0.480 5.468 10012 Z= 0.242 Chirality : 0.041 0.161 1218 Planarity : 0.004 0.053 1263 Dihedral : 6.468 88.990 1042 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 1.50 % Allowed : 19.37 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 940 helix: 1.40 (0.34), residues: 283 sheet: -0.37 (0.35), residues: 213 loop : -0.68 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2426 HIS 0.008 0.001 HIS A2391 PHE 0.019 0.001 PHE A1792 TYR 0.007 0.001 TYR A2018 ARG 0.007 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.861 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 108 average time/residue: 0.1962 time to fit residues: 29.3223 Evaluate side-chains 96 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0852 time to fit residues: 1.5167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1657 GLN A2505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7377 Z= 0.198 Angle : 0.529 7.967 10012 Z= 0.264 Chirality : 0.043 0.182 1218 Planarity : 0.004 0.052 1263 Dihedral : 6.627 91.083 1042 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 0.75 % Allowed : 20.42 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 940 helix: 1.26 (0.33), residues: 285 sheet: -0.43 (0.35), residues: 213 loop : -0.63 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2316 HIS 0.007 0.001 HIS A2391 PHE 0.012 0.001 PHE A2059 TYR 0.020 0.001 TYR A1739 ARG 0.009 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.787 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.1735 time to fit residues: 21.8927 Evaluate side-chains 86 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0703 time to fit residues: 1.4378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1998 HIS A2505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7377 Z= 0.221 Angle : 0.550 8.327 10012 Z= 0.276 Chirality : 0.043 0.177 1218 Planarity : 0.004 0.052 1263 Dihedral : 6.682 89.820 1042 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 0.60 % Allowed : 21.02 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 940 helix: 1.14 (0.33), residues: 285 sheet: -0.53 (0.35), residues: 213 loop : -0.63 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2426 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.021 0.001 TYR A1739 ARG 0.008 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.900 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 0.2060 time to fit residues: 24.6664 Evaluate side-chains 83 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0707 time to fit residues: 1.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7377 Z= 0.136 Angle : 0.514 8.110 10012 Z= 0.260 Chirality : 0.042 0.179 1218 Planarity : 0.004 0.052 1263 Dihedral : 6.521 87.349 1042 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 0.45 % Allowed : 20.57 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 940 helix: 1.43 (0.34), residues: 283 sheet: -0.34 (0.35), residues: 213 loop : -0.59 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.010 0.001 PHE A2059 TYR 0.016 0.001 TYR A2018 ARG 0.009 0.000 ARG A2339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1851 time to fit residues: 23.7691 Evaluate side-chains 87 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.136560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.115538 restraints weight = 14862.347| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.50 r_work: 0.3759 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7377 Z= 0.291 Angle : 0.594 9.078 10012 Z= 0.299 Chirality : 0.044 0.181 1218 Planarity : 0.005 0.051 1263 Dihedral : 6.744 91.061 1042 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.28 % Favored : 93.62 % Rotamer: Outliers : 0.30 % Allowed : 20.57 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.28), residues: 940 helix: 1.00 (0.33), residues: 288 sheet: -0.60 (0.35), residues: 208 loop : -0.68 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.016 0.002 PHE A2059 TYR 0.023 0.002 TYR A1739 ARG 0.007 0.001 ARG A2339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.98 seconds wall clock time: 34 minutes 30.48 seconds (2070.48 seconds total)