Starting phenix.real_space_refine on Sat Aug 3 01:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k88_36947/08_2024/8k88_36947.cif" } resolution = 2.6 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= 0.005 sd= 0.050 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4124 2.51 5 N 1150 2.21 5 O 1345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6686 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.70 Number of scatterers: 6686 At special positions: 0 Unit cell: (74.6512, 90.2876, 107.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 44 15.00 Mg 1 11.99 O 1345 8.00 N 1150 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.01 Conformation dependent library (CDL) restraints added in 978.8 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.7% alpha, 24.1% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.883A pdb=" N CYS A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.735A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.949A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.705A pdb=" N ARG A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.920A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.891A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.680A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.634A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 4.266A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.024A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.601A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.968A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.156A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.324A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.190A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.624A pdb=" N ALA A 355 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.262A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.739A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 382 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ARG B 344 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 343 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR B 403 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 345 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN B 401 " --> pdb=" O CYS B 345 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 347 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 399 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 349 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 556 through 561 271 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1887 1.34 - 1.45: 1374 1.45 - 1.57: 3555 1.57 - 1.69: 86 1.69 - 1.81: 32 Bond restraints: 6934 Sorted by residual: bond pdb=" CB GLU B 566 " pdb=" CG GLU B 566 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 bond pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" C3' DA C 15 " pdb=" C2' DA C 15 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.00e+00 ... (remaining 6929 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 468 107.25 - 113.93: 3859 113.93 - 120.61: 2748 120.61 - 127.29: 2376 127.29 - 133.97: 143 Bond angle restraints: 9594 Sorted by residual: angle pdb=" C SER B 327 " pdb=" N PHE B 328 " pdb=" CA PHE B 328 " ideal model delta sigma weight residual 121.48 127.26 -5.78 2.04e+00 2.40e-01 8.02e+00 angle pdb=" CA GLU B 496 " pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.71e+00 angle pdb=" CA LEU A 146 " pdb=" CB LEU A 146 " pdb=" CG LEU A 146 " ideal model delta sigma weight residual 116.30 125.18 -8.88 3.50e+00 8.16e-02 6.43e+00 angle pdb=" CB GLU B 566 " pdb=" CG GLU B 566 " pdb=" CD GLU B 566 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.70e+00 3.46e-01 6.38e+00 angle pdb=" CB MET B 504 " pdb=" CG MET B 504 " pdb=" SD MET B 504 " ideal model delta sigma weight residual 112.70 120.22 -7.52 3.00e+00 1.11e-01 6.29e+00 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 3828 34.39 - 68.77: 273 68.77 - 103.16: 14 103.16 - 137.54: 1 137.54 - 171.93: 1 Dihedral angle restraints: 4117 sinusoidal: 2007 harmonic: 2110 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 11.93 -171.93 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " pdb=" NE ARG A 69 " pdb=" CZ ARG A 69 " ideal model delta sinusoidal sigma weight residual -90.00 -37.10 -52.90 2 1.50e+01 4.44e-03 1.36e+01 dihedral pdb=" C4' DT C 13 " pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " pdb=" P DA C 14 " ideal model delta sinusoidal sigma weight residual 220.00 103.43 116.57 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 4114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 708 0.029 - 0.059: 250 0.059 - 0.088: 55 0.088 - 0.117: 56 0.117 - 0.146: 5 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C1' G D 15 " pdb=" O4' G D 15 " pdb=" C2' G D 15 " pdb=" N9 G D 15 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA THR A 242 " pdb=" N THR A 242 " pdb=" C THR A 242 " pdb=" CB THR A 242 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1071 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 389 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 390 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.68e+00 pdb=" N9 A D 4 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 401 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 402 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.029 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 44 2.56 - 3.14: 4837 3.14 - 3.73: 10670 3.73 - 4.31: 15184 4.31 - 4.90: 24623 Nonbonded interactions: 55358 Sorted by model distance: nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.973 2.170 nonbonded pdb=" OP1 A D 3 " pdb="MG MG A 501 " model vdw 1.987 2.170 nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 2.070 2.170 nonbonded pdb=" O THR A 242 " pdb=" OG1 THR A 262 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 195 " pdb=" ND2 ASN A 436 " model vdw 2.212 3.120 ... (remaining 55353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.770 Find NCS groups from input model: 0.060 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.002 0.034 6934 Z= 0.149 Angle : 0.578 8.877 9594 Z= 0.310 Chirality : 0.038 0.146 1074 Planarity : 0.005 0.065 1076 Dihedral : 20.288 171.926 2761 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.96 % Allowed : 27.97 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.49 (0.32), residues: 722 helix: 2.27 (0.35), residues: 221 sheet: 0.96 (0.40), residues: 180 loop : 0.16 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 PHE 0.008 0.001 PHE A 137 TYR 0.022 0.001 TYR A 341 ARG 0.010 0.001 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.679 Fit side-chains REVERT: A 156 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8197 (ptmm) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 1.4204 time to fit residues: 285.4300 Evaluate side-chains 188 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6934 Z= 0.137 Angle : 0.524 7.630 9594 Z= 0.276 Chirality : 0.039 0.130 1074 Planarity : 0.005 0.052 1076 Dihedral : 18.364 170.167 1379 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.22 % Allowed : 23.47 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.62 (0.33), residues: 722 helix: 2.42 (0.35), residues: 222 sheet: 0.96 (0.41), residues: 180 loop : 0.25 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.004 0.001 HIS B 437 PHE 0.015 0.001 PHE A 143 TYR 0.015 0.001 TYR A 366 ARG 0.007 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 0.689 Fit side-chains REVERT: B 557 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8451 (p) outliers start: 20 outliers final: 8 residues processed: 199 average time/residue: 1.4116 time to fit residues: 292.5170 Evaluate side-chains 198 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6934 Z= 0.173 Angle : 0.513 5.820 9594 Z= 0.270 Chirality : 0.039 0.135 1074 Planarity : 0.005 0.046 1076 Dihedral : 18.256 166.726 1371 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.22 % Allowed : 23.63 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.59 (0.32), residues: 722 helix: 2.44 (0.35), residues: 222 sheet: 0.89 (0.41), residues: 180 loop : 0.23 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 PHE 0.013 0.001 PHE A 304 TYR 0.014 0.001 TYR A 366 ARG 0.009 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 0.735 Fit side-chains REVERT: B 358 GLU cc_start: 0.7569 (tp30) cc_final: 0.7364 (tp30) REVERT: B 504 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7808 (mmm) REVERT: B 557 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8450 (p) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 1.4578 time to fit residues: 288.2242 Evaluate side-chains 196 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6934 Z= 0.164 Angle : 0.507 5.914 9594 Z= 0.266 Chirality : 0.039 0.138 1074 Planarity : 0.004 0.041 1076 Dihedral : 18.143 165.911 1371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.73 % Allowed : 23.95 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.63 (0.33), residues: 722 helix: 2.51 (0.35), residues: 222 sheet: 0.92 (0.41), residues: 180 loop : 0.22 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 PHE 0.013 0.001 PHE A 304 TYR 0.014 0.001 TYR A 366 ARG 0.010 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 0.733 Fit side-chains REVERT: B 504 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7807 (mmm) outliers start: 17 outliers final: 12 residues processed: 194 average time/residue: 1.3849 time to fit residues: 280.1674 Evaluate side-chains 201 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6934 Z= 0.229 Angle : 0.522 5.938 9594 Z= 0.275 Chirality : 0.040 0.148 1074 Planarity : 0.004 0.039 1076 Dihedral : 18.210 168.462 1371 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.22 % Allowed : 23.47 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.55 (0.32), residues: 722 helix: 2.44 (0.35), residues: 222 sheet: 0.90 (0.41), residues: 180 loop : 0.16 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 PHE 0.013 0.001 PHE A 304 TYR 0.015 0.001 TYR A 366 ARG 0.009 0.001 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 0.730 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 1.4099 time to fit residues: 281.9426 Evaluate side-chains 196 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6934 Z= 0.163 Angle : 0.511 5.925 9594 Z= 0.269 Chirality : 0.039 0.142 1074 Planarity : 0.004 0.046 1076 Dihedral : 18.140 166.524 1371 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 24.76 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.58 (0.33), residues: 722 helix: 2.48 (0.35), residues: 222 sheet: 0.91 (0.41), residues: 180 loop : 0.18 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.000 HIS A 166 PHE 0.011 0.001 PHE A 304 TYR 0.013 0.001 TYR A 366 ARG 0.011 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 0.718 Fit side-chains REVERT: A 55 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (tt) outliers start: 16 outliers final: 12 residues processed: 190 average time/residue: 1.5193 time to fit residues: 300.6494 Evaluate side-chains 193 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6934 Z= 0.151 Angle : 0.505 5.915 9594 Z= 0.267 Chirality : 0.039 0.139 1074 Planarity : 0.004 0.041 1076 Dihedral : 18.127 165.591 1371 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 24.60 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.60 (0.33), residues: 722 helix: 2.54 (0.35), residues: 222 sheet: 0.83 (0.41), residues: 180 loop : 0.21 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.000 HIS A 166 PHE 0.019 0.001 PHE B 579 TYR 0.014 0.001 TYR A 366 ARG 0.010 0.001 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 0.694 Fit side-chains REVERT: A 55 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (tt) outliers start: 16 outliers final: 12 residues processed: 185 average time/residue: 1.4879 time to fit residues: 286.2951 Evaluate side-chains 192 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.0030 chunk 69 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6934 Z= 0.155 Angle : 0.503 5.850 9594 Z= 0.266 Chirality : 0.039 0.138 1074 Planarity : 0.004 0.042 1076 Dihedral : 18.108 164.313 1371 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 24.92 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.61 (0.33), residues: 722 helix: 2.56 (0.35), residues: 222 sheet: 0.84 (0.41), residues: 180 loop : 0.21 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 11 PHE 0.020 0.001 PHE B 579 TYR 0.014 0.001 TYR A 366 ARG 0.010 0.001 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.714 Fit side-chains REVERT: A 55 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 191 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7819 (mm-40) REVERT: A 450 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: B 504 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7781 (mmm) outliers start: 17 outliers final: 13 residues processed: 182 average time/residue: 1.4687 time to fit residues: 278.0259 Evaluate side-chains 194 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6934 Z= 0.191 Angle : 0.516 6.239 9594 Z= 0.271 Chirality : 0.040 0.142 1074 Planarity : 0.004 0.042 1076 Dihedral : 18.125 165.022 1371 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.89 % Allowed : 24.76 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.57 (0.32), residues: 722 helix: 2.53 (0.35), residues: 222 sheet: 0.82 (0.41), residues: 180 loop : 0.17 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 11 PHE 0.020 0.001 PHE A 257 TYR 0.014 0.001 TYR A 366 ARG 0.010 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 0.642 Fit side-chains REVERT: A 144 ASP cc_start: 0.8245 (m-30) cc_final: 0.7961 (m-30) REVERT: A 450 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 454 ASP cc_start: 0.8246 (m-30) cc_final: 0.8032 (m-30) REVERT: B 576 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7912 (ttt-90) outliers start: 18 outliers final: 12 residues processed: 194 average time/residue: 1.4424 time to fit residues: 291.3743 Evaluate side-chains 193 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6934 Z= 0.236 Angle : 0.534 5.946 9594 Z= 0.280 Chirality : 0.040 0.149 1074 Planarity : 0.004 0.041 1076 Dihedral : 18.203 168.245 1371 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.09 % Allowed : 25.56 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.42 (0.32), residues: 722 helix: 2.40 (0.35), residues: 222 sheet: 0.70 (0.42), residues: 174 loop : 0.11 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 PHE 0.019 0.001 PHE A 257 TYR 0.014 0.001 TYR A 366 ARG 0.009 0.001 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 0.720 Fit side-chains REVERT: B 326 LYS cc_start: 0.5773 (pttm) cc_final: 0.5319 (pttm) outliers start: 13 outliers final: 11 residues processed: 189 average time/residue: 1.4920 time to fit residues: 293.7874 Evaluate side-chains 197 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107151 restraints weight = 8981.048| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.57 r_work: 0.3349 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6934 Z= 0.177 Angle : 0.528 6.653 9594 Z= 0.278 Chirality : 0.039 0.143 1074 Planarity : 0.005 0.061 1076 Dihedral : 18.123 165.184 1371 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.77 % Allowed : 25.88 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.46 (0.32), residues: 722 helix: 2.47 (0.35), residues: 222 sheet: 0.72 (0.42), residues: 174 loop : 0.12 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 PHE 0.022 0.001 PHE B 579 TYR 0.013 0.001 TYR A 366 ARG 0.015 0.001 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.68 seconds wall clock time: 80 minutes 45.76 seconds (4845.76 seconds total)