Starting phenix.real_space_refine on Sun May 18 19:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407.map" model { file = "/net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ban_44407/05_2025/9ban_44407_neut.cif" } resolution = 3.39 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= 0.000 sd= 0.005 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 45 5.16 5 C 5545 2.51 5 N 1516 2.21 5 O 1715 1.98 5 H 8684 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17505 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1405 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1546 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 1527 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 102, 1527 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1521 Chain: "C" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 340 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1458 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 97, 1439 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 97, 1439 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1431 Chain: "E" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3141 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3242 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202} Chain: "G" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3131 Classifications: {'peptide': 212} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU%NH1NOTPRO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3242 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202} Time building chain proxies: 12.31, per 1000 atoms: 0.70 Number of scatterers: 17505 At special positions: 0 Unit cell: (88.102, 100.688, 132.602, 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 45 16.00 O 1715 8.00 N 1516 7.00 C 5545 6.00 H 8684 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 492 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 492 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 115 " distance=2.04 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 221 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 108 " distance=2.04 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 213 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 115 " distance=2.04 Simple disulfide: pdb=" SG CYS G 166 " - pdb=" SG CYS G 221 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 26 sheets defined 12.4% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 376 through 393 removed outlier: 3.692A pdb=" N ALA A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.904A pdb=" N ALA A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 517 removed outlier: 3.826A pdb=" N GLY B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'D' and resid 504 through 517 removed outlier: 3.699A pdb=" N GLY D 517 " --> pdb=" O MET D 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 202 through 208 removed outlier: 3.793A pdb=" N HIS F 208 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 202 through 208 removed outlier: 3.553A pdb=" N ARG H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS H 208 " --> pdb=" O GLU H 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 463 through 465 Processing sheet with id=AA2, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AA3, first strand: chain 'B' and resid 477 through 479 removed outlier: 6.162A pdb=" N ALA B 532 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 551 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.580A pdb=" N ALA B 519 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA G 125 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.580A pdb=" N ALA B 519 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA G 125 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 68 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS G 57 " --> pdb=" O TRP G 66 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TRP G 66 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG G 59 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU G 64 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 525 through 528 removed outlier: 3.649A pdb=" N VAL B 527 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 463 through 465 Processing sheet with id=AA8, first strand: chain 'D' and resid 468 through 470 Processing sheet with id=AA9, first strand: chain 'D' and resid 477 through 479 removed outlier: 6.113A pdb=" N ALA D 532 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 551 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 519 through 520 removed outlier: 3.563A pdb=" N ALA D 519 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA E 125 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 519 through 520 removed outlier: 3.563A pdb=" N ALA D 519 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA E 125 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 68 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS E 57 " --> pdb=" O TRP E 66 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TRP E 66 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG E 59 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 64 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 525 through 528 removed outlier: 3.657A pdb=" N VAL D 527 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.593A pdb=" N GLY E 165 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'F' and resid 24 through 27 removed outlier: 3.642A pdb=" N PHE F 91 " --> pdb=" O CYS F 43 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP F 90 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 68 removed outlier: 5.585A pdb=" N LEU F 66 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN F 57 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 133 through 137 Processing sheet with id=AC1, first strand: chain 'F' and resid 173 through 174 removed outlier: 3.713A pdb=" N ARG F 174 " --> pdb=" O TRP F 167 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP F 167 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC3, first strand: chain 'G' and resid 146 through 150 removed outlier: 3.583A pdb=" N GLY G 165 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 177 through 180 Processing sheet with id=AC5, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.632A pdb=" N PHE H 91 " --> pdb=" O CYS H 43 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP H 90 " --> pdb=" O TYR H 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 65 through 68 removed outlier: 5.630A pdb=" N LEU H 66 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN H 57 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 133 through 137 Processing sheet with id=AC8, first strand: chain 'H' and resid 164 through 169 343 hydrogen bonds defined for protein. 903 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: 6.04 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8685 1.03 - 1.23: 354 1.23 - 1.43: 3390 1.43 - 1.63: 5208 1.63 - 1.83: 59 Bond restraints: 17696 Sorted by residual: bond pdb=" C ASN F 73 " pdb=" O ASN F 73 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.14e-02 7.69e+03 4.07e+01 bond pdb=" CA TYR F 75 " pdb=" C TYR F 75 " ideal model delta sigma weight residual 1.523 1.455 0.069 1.34e-02 5.57e+03 2.62e+01 bond pdb=" N GLU G 20 " pdb=" H1 GLU G 20 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C TYR F 75 " pdb=" O TYR F 75 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.26e-02 6.30e+03 2.06e+01 bond pdb=" N SER F 21 " pdb=" H3 SER F 21 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 31930 5.11 - 10.21: 7 10.21 - 15.32: 2 15.32 - 20.42: 2 20.42 - 25.53: 1 Bond angle restraints: 31942 Sorted by residual: angle pdb=" H1 SER F 21 " pdb=" N SER F 21 " pdb=" H3 SER F 21 " ideal model delta sigma weight residual 109.47 83.94 25.53 3.00e+00 1.11e-01 7.24e+01 angle pdb=" CA SER F 72 " pdb=" C SER F 72 " pdb=" N ASN F 73 " ideal model delta sigma weight residual 115.92 124.16 -8.24 1.28e+00 6.10e-01 4.14e+01 angle pdb=" N ASN F 73 " pdb=" CA ASN F 73 " pdb=" C ASN F 73 " ideal model delta sigma weight residual 108.34 100.44 7.90 1.31e+00 5.83e-01 3.64e+01 angle pdb=" H1 SER F 21 " pdb=" N SER F 21 " pdb=" H2 SER F 21 " ideal model delta sigma weight residual 109.47 126.43 -16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" H1 SER H 21 " pdb=" N SER H 21 " pdb=" H3 SER H 21 " ideal model delta sigma weight residual 109.47 92.71 16.76 3.00e+00 1.11e-01 3.12e+01 ... (remaining 31937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7538 16.84 - 33.68: 679 33.68 - 50.52: 225 50.52 - 67.35: 49 67.35 - 84.19: 14 Dihedral angle restraints: 8505 sinusoidal: 4611 harmonic: 3894 Sorted by residual: dihedral pdb=" CB CYS G 166 " pdb=" SG CYS G 166 " pdb=" SG CYS G 221 " pdb=" CB CYS G 221 " ideal model delta sinusoidal sigma weight residual 93.00 56.45 36.55 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS E 166 " pdb=" SG CYS E 166 " pdb=" SG CYS E 221 " pdb=" CB CYS E 221 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" NE ARG F 74 " pdb=" CZ ARG F 74 " pdb=" NH1 ARG F 74 " pdb="HH12 ARG F 74 " ideal model delta sinusoidal sigma weight residual 0.00 76.47 -76.47 2 2.00e+01 2.50e-03 1.13e+01 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 821 0.030 - 0.060: 414 0.060 - 0.090: 80 0.090 - 0.120: 79 0.120 - 0.150: 32 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA ILE F 41 " pdb=" N ILE F 41 " pdb=" C ILE F 41 " pdb=" CB ILE F 41 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ILE E 119 " pdb=" N ILE E 119 " pdb=" C ILE E 119 " pdb=" CB ILE E 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE F 163 " pdb=" N ILE F 163 " pdb=" C ILE F 163 " pdb=" CB ILE F 163 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1423 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 74 " -0.412 9.50e-02 1.11e+02 3.73e-01 2.73e+03 pdb=" NE ARG F 74 " -0.124 2.00e-02 2.50e+03 pdb=" CZ ARG F 74 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG F 74 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 74 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG F 74 " -0.706 2.00e-02 2.50e+03 pdb="HH12 ARG F 74 " 0.750 2.00e-02 2.50e+03 pdb="HH21 ARG F 74 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG F 74 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 73 " -0.244 2.00e-02 2.50e+03 3.21e-01 1.55e+03 pdb=" CG ASN F 73 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN F 73 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN F 73 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN F 73 " 0.499 2.00e-02 2.50e+03 pdb="HD22 ASN F 73 " -0.494 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG G 59 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO G 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.030 5.00e-02 4.00e+02 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3010 2.28 - 2.86: 37270 2.86 - 3.44: 37530 3.44 - 4.02: 54528 4.02 - 4.60: 81576 Nonbonded interactions: 213914 Sorted by model distance: nonbonded pdb=" OE1 GLU B 541 " pdb=" H GLU B 541 " model vdw 1.697 2.450 nonbonded pdb=" HE ARG A 312 " pdb=" OD1 ASP B 470 " model vdw 1.713 2.450 nonbonded pdb="HD22 ASN H 209 " pdb=" OD1 ASN H 231 " model vdw 1.715 2.450 nonbonded pdb=" OD1 ASP F 203 " pdb=" H GLU F 204 " model vdw 1.729 2.450 nonbonded pdb=" OD1 ASP H 203 " pdb=" H GLU H 204 " model vdw 1.757 2.450 ... (remaining 213909 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 459 through 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 476 through 501 or re \ sid 503 through 540 or resid 544 through 560)) selection = (chain 'D' and (resid 459 through 501 or resid 503 through 560)) } ncs_group { reference = (chain 'E' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name H1 or name HA )) or resid 21 through 238)) selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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=0.35 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: 15.800 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: 0.310 Extract box with map and model: 0.760 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.510 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.073 9024 Z= 0.195 Angle : 0.614 8.239 12304 Z= 0.340 Chirality : 0.044 0.150 1426 Planarity : 0.004 0.089 1565 Dihedral : 14.568 84.192 3236 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.51 (0.26), residues: 1134 helix: 2.54 (0.48), residues: 117 sheet: 0.50 (0.24), residues: 513 loop : -2.03 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 182 HIS 0.003 0.001 HIS B 506 PHE 0.013 0.002 PHE F 228 TYR 0.019 0.001 TYR F 69 ARG 0.004 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.09204 ( 335) hydrogen bonds : angle 4.50295 ( 903) SS BOND : bond 0.00650 ( 14) SS BOND : angle 1.69801 ( 28) covalent geometry : bond 0.00370 ( 9010) covalent geometry : angle 0.60961 (12276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.6161 time to fit residues: 70.6874 Evaluate side-chains 77 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 514 GLN F 209 ASN H 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127391 restraints weight = 39964.311| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.48 r_work: 0.3427 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9024 Z= 0.098 Angle : 0.512 4.436 12304 Z= 0.269 Chirality : 0.042 0.164 1426 Planarity : 0.004 0.052 1565 Dihedral : 4.036 25.224 1253 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.23 % Allowed : 18.36 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.42 (0.26), residues: 1134 helix: 2.71 (0.46), residues: 117 sheet: 0.57 (0.24), residues: 515 loop : -2.02 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.002 0.001 HIS H 208 PHE 0.008 0.001 PHE F 228 TYR 0.009 0.001 TYR G 114 ARG 0.003 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 335) hydrogen bonds : angle 4.20326 ( 903) SS BOND : bond 0.00523 ( 14) SS BOND : angle 1.15580 ( 28) covalent geometry : bond 0.00227 ( 9010) covalent geometry : angle 0.51005 (12276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ASP cc_start: 0.8080 (p0) cc_final: 0.7855 (p0) REVERT: F 209 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (t0) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.5062 time to fit residues: 64.0486 Evaluate side-chains 87 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN H 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122656 restraints weight = 41343.168| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.53 r_work: 0.3352 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.109 Angle : 0.507 3.829 12304 Z= 0.268 Chirality : 0.042 0.154 1426 Planarity : 0.004 0.052 1565 Dihedral : 4.002 16.693 1253 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.64 % Allowed : 18.15 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.34 (0.26), residues: 1134 helix: 3.02 (0.46), residues: 117 sheet: 0.60 (0.24), residues: 515 loop : -2.01 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.003 0.001 HIS F 208 PHE 0.010 0.001 PHE F 158 TYR 0.010 0.001 TYR G 114 ARG 0.002 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 335) hydrogen bonds : angle 4.19704 ( 903) SS BOND : bond 0.00613 ( 14) SS BOND : angle 1.24909 ( 28) covalent geometry : bond 0.00261 ( 9010) covalent geometry : angle 0.50376 (12276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ASP cc_start: 0.8106 (p0) cc_final: 0.7880 (p0) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.4908 time to fit residues: 61.6879 Evaluate side-chains 90 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 0.0000 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN H 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123440 restraints weight = 34965.174| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.18 r_work: 0.3352 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.144 Angle : 0.535 4.129 12304 Z= 0.285 Chirality : 0.043 0.152 1426 Planarity : 0.004 0.053 1565 Dihedral : 4.190 20.396 1253 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.95 % Allowed : 17.33 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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 (0.26), residues: 1134 helix: 2.87 (0.46), residues: 120 sheet: 0.55 (0.24), residues: 515 loop : -2.10 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.007 0.001 HIS H 208 PHE 0.012 0.001 PHE F 93 TYR 0.010 0.001 TYR G 114 ARG 0.002 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 335) hydrogen bonds : angle 4.29608 ( 903) SS BOND : bond 0.00741 ( 14) SS BOND : angle 1.42268 ( 28) covalent geometry : bond 0.00347 ( 9010) covalent geometry : angle 0.53172 (12276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 203 ASP cc_start: 0.8084 (p0) cc_final: 0.7845 (p0) outliers start: 19 outliers final: 17 residues processed: 98 average time/residue: 0.5134 time to fit residues: 68.9167 Evaluate side-chains 95 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 1 optimal weight: 0.0050 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 73 ASN F 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125586 restraints weight = 34934.042| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.12 r_work: 0.3395 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9024 Z= 0.109 Angle : 0.506 3.859 12304 Z= 0.268 Chirality : 0.043 0.152 1426 Planarity : 0.004 0.053 1565 Dihedral : 4.085 18.443 1253 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.15 % Allowed : 17.54 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.38 (0.26), residues: 1134 helix: 2.99 (0.46), residues: 120 sheet: 0.54 (0.24), residues: 515 loop : -2.03 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.003 0.001 HIS G 54 PHE 0.011 0.001 PHE F 228 TYR 0.008 0.001 TYR H 69 ARG 0.002 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 335) hydrogen bonds : angle 4.23784 ( 903) SS BOND : bond 0.00627 ( 14) SS BOND : angle 1.28759 ( 28) covalent geometry : bond 0.00262 ( 9010) covalent geometry : angle 0.50290 (12276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 488 CYS cc_start: 0.7807 (m) cc_final: 0.7600 (m) REVERT: F 203 ASP cc_start: 0.8085 (p0) cc_final: 0.7834 (p0) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.4916 time to fit residues: 67.6368 Evaluate side-chains 99 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125457 restraints weight = 41088.324| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.34 r_work: 0.3390 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9024 Z= 0.094 Angle : 0.485 4.266 12304 Z= 0.255 Chirality : 0.042 0.147 1426 Planarity : 0.004 0.052 1565 Dihedral : 3.972 17.005 1253 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.26 % Allowed : 17.54 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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 (0.26), residues: 1134 helix: 3.02 (0.47), residues: 120 sheet: 0.58 (0.24), residues: 515 loop : -2.00 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.002 0.000 HIS G 54 PHE 0.009 0.001 PHE H 93 TYR 0.007 0.001 TYR H 69 ARG 0.002 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 335) hydrogen bonds : angle 4.15106 ( 903) SS BOND : bond 0.00547 ( 14) SS BOND : angle 1.10958 ( 28) covalent geometry : bond 0.00222 ( 9010) covalent geometry : angle 0.48255 (12276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 203 ASP cc_start: 0.8090 (p0) cc_final: 0.7864 (p0) outliers start: 22 outliers final: 18 residues processed: 100 average time/residue: 0.4834 time to fit residues: 66.7198 Evaluate side-chains 99 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123733 restraints weight = 46558.047| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.72 r_work: 0.3343 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9024 Z= 0.093 Angle : 0.483 4.480 12304 Z= 0.254 Chirality : 0.042 0.148 1426 Planarity : 0.004 0.052 1565 Dihedral : 3.908 16.695 1253 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.15 % Allowed : 18.46 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.26 (0.26), residues: 1134 helix: 3.11 (0.47), residues: 120 sheet: 0.60 (0.24), residues: 505 loop : -1.88 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.002 0.001 HIS G 54 PHE 0.009 0.001 PHE F 228 TYR 0.007 0.001 TYR H 69 ARG 0.002 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 335) hydrogen bonds : angle 4.09348 ( 903) SS BOND : bond 0.00557 ( 14) SS BOND : angle 1.14974 ( 28) covalent geometry : bond 0.00222 ( 9010) covalent geometry : angle 0.48032 (12276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: B 513 MET cc_start: 0.8605 (tpp) cc_final: 0.8362 (ttm) REVERT: F 203 ASP cc_start: 0.8154 (p0) cc_final: 0.7921 (p0) outliers start: 21 outliers final: 21 residues processed: 101 average time/residue: 0.4654 time to fit residues: 64.2778 Evaluate side-chains 103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.145961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122884 restraints weight = 38771.793| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.29 r_work: 0.3352 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9024 Z= 0.149 Angle : 0.531 4.153 12304 Z= 0.283 Chirality : 0.043 0.147 1426 Planarity : 0.004 0.052 1565 Dihedral : 4.151 20.111 1253 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.67 % Allowed : 17.85 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.40 (0.26), residues: 1134 helix: 2.90 (0.46), residues: 120 sheet: 0.53 (0.24), residues: 515 loop : -2.04 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.003 0.001 HIS G 54 PHE 0.013 0.001 PHE F 93 TYR 0.010 0.001 TYR E 114 ARG 0.004 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 335) hydrogen bonds : angle 4.27668 ( 903) SS BOND : bond 0.00734 ( 14) SS BOND : angle 1.57094 ( 28) covalent geometry : bond 0.00366 ( 9010) covalent geometry : angle 0.52647 (12276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 1.391 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 24 residues processed: 103 average time/residue: 0.4746 time to fit residues: 67.2146 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124028 restraints weight = 39534.041| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.32 r_work: 0.3372 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 0.036 9024 Z= 0.112 Angle : 0.508 5.213 12304 Z= 0.269 Chirality : 0.043 0.148 1426 Planarity : 0.004 0.052 1565 Dihedral : 4.093 18.958 1253 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.36 % Allowed : 18.46 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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 (0.26), residues: 1134 helix: 2.89 (0.46), residues: 120 sheet: 0.55 (0.24), residues: 505 loop : -1.93 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.003 0.001 HIS G 54 PHE 0.010 0.001 PHE F 93 TYR 0.008 0.001 TYR H 69 ARG 0.003 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 335) hydrogen bonds : angle 4.21320 ( 903) SS BOND : bond 0.00630 ( 14) SS BOND : angle 1.34700 ( 28) covalent geometry : bond 0.00271 ( 9010) covalent geometry : angle 0.50450 (12276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: F 225 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8343 (p) outliers start: 23 outliers final: 21 residues processed: 100 average time/residue: 0.4831 time to fit residues: 66.0991 Evaluate side-chains 102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 8 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN G 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126913 restraints weight = 38073.443| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.28 r_work: 0.3409 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9024 Z= 0.084 Angle : 0.473 3.884 12304 Z= 0.248 Chirality : 0.042 0.151 1426 Planarity : 0.004 0.051 1565 Dihedral : 3.885 15.659 1253 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.64 % Allowed : 18.97 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.28 (0.26), residues: 1134 helix: 3.17 (0.48), residues: 117 sheet: 0.67 (0.25), residues: 469 loop : -1.82 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 494 HIS 0.002 0.000 HIS G 54 PHE 0.008 0.001 PHE H 93 TYR 0.007 0.001 TYR H 69 ARG 0.002 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.02610 ( 335) hydrogen bonds : angle 4.05094 ( 903) SS BOND : bond 0.00438 ( 14) SS BOND : angle 1.04741 ( 28) covalent geometry : bond 0.00197 ( 9010) covalent geometry : angle 0.47062 (12276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 422 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 473 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: H 143 GLN cc_start: 0.8291 (tp40) cc_final: 0.7540 (tt0) outliers start: 16 outliers final: 15 residues processed: 90 average time/residue: 0.5024 time to fit residues: 61.9234 Evaluate side-chains 90 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 overall best weight: 0.5950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123611 restraints weight = 40891.710| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.57 r_work: 0.3377 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9024 Z= 0.088 Angle : 0.477 5.317 12304 Z= 0.250 Chirality : 0.042 0.149 1426 Planarity : 0.004 0.052 1565 Dihedral : 3.832 15.475 1253 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.64 % Allowed : 19.18 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.19 (0.26), residues: 1134 helix: 3.22 (0.48), residues: 117 sheet: 0.60 (0.24), residues: 505 loop : -1.78 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 494 HIS 0.002 0.000 HIS G 54 PHE 0.008 0.001 PHE H 93 TYR 0.006 0.001 TYR H 69 ARG 0.003 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 335) hydrogen bonds : angle 4.01952 ( 903) SS BOND : bond 0.00480 ( 14) SS BOND : angle 1.11476 ( 28) covalent geometry : bond 0.00210 ( 9010) covalent geometry : angle 0.47447 (12276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9578.20 seconds wall clock time: 165 minutes 42.00 seconds (9942.00 seconds total)