Starting phenix.real_space_refine on Sat Oct 11 08:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041.map" model { file = "/net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u9y_42041/10_2025/8u9y_42041_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4235 2.51 5 N 1142 2.21 5 O 1347 1.98 5 H 6188 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12951 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3589 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 224} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3174 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3129 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1457 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1418 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.09, per 1000 atoms: 0.24 Number of scatterers: 12951 At special positions: 0 Unit cell: (110.88, 133.28, 98.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1347 8.00 N 1142 7.00 C 4235 6.00 H 6188 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 452 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 552 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS M 133 " - pdb=" SG CYS M 193 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 201 " distance=2.03 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 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A 701 " - " ASN A 430 " " NAG A 702 " - " ASN A 448 " " NAG B 1 " - " ASN A 423 " " NAG C 1 " - " ASN A 532 " " NAG D 1 " - " ASN A 540 " " NAG G 1 " - " ASN A 556 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 481.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 19 sheets defined 10.9% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.152A pdb=" N PHE A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.820A pdb=" N SER A 450 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.065A pdb=" N ARG A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 619 through 622 removed outlier: 3.967A pdb=" N VAL A 622 " --> pdb=" O PRO A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 206 through 209 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.884A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.602A pdb=" N SER F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'N' and resid 159 through 163 Processing helix chain 'N' and resid 191 through 196 Processing helix chain 'N' and resid 207 through 209 No H-bonds generated for 'chain 'N' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427 removed outlier: 4.555A pdb=" N ALA A 426 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.212A pdb=" N THR A 473 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 516 removed outlier: 4.340A pdb=" N VAL A 506 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 507 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 509 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 551 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 607 through 608 Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.517A pdb=" N ALA E 92 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.975A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL E 147 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER E 182 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA E 173 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER E 184 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 171 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.533A pdb=" N THR E 156 " --> pdb=" O ASN E 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.614A pdb=" N SER F 33 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AB3, first strand: chain 'F' and resid 17 through 23 Processing sheet with id=AB4, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.718A pdb=" N SER F 113 " --> pdb=" O ASN F 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 144 through 149 Processing sheet with id=AB6, first strand: chain 'M' and resid 114 through 117 removed outlier: 3.757A pdb=" N VAL M 132 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN M 137 " --> pdb=" O TYR M 172 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR M 172 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 153 through 154 removed outlier: 4.419A pdb=" N TRP M 147 " --> pdb=" O GLN M 154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS M 144 " --> pdb=" O THR M 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 127 through 129 removed outlier: 6.373A pdb=" N TYR N 181 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 127 through 129 removed outlier: 6.373A pdb=" N TYR N 181 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 155 through 158 236 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2319 1.02 - 1.22: 3872 1.22 - 1.42: 2951 1.42 - 1.63: 3940 1.63 - 1.83: 46 Bond restraints: 13128 Sorted by residual: bond pdb=" NE1 TRP E 159 " pdb=" HE1 TRP E 159 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP A 602 " pdb=" HE1 TRP A 602 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP A 616 " pdb=" HE1 TRP A 616 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP A 529 " pdb=" HE1 TRP A 529 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP M 147 " pdb=" HE1 TRP M 147 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 13123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 21346 2.02 - 4.04: 2041 4.04 - 6.06: 121 6.06 - 8.08: 23 8.08 - 10.10: 8 Bond angle restraints: 23539 Sorted by residual: angle pdb=" N ASN N 209 " pdb=" CA ASN N 209 " pdb=" C ASN N 209 " ideal model delta sigma weight residual 111.39 102.00 9.39 1.38e+00 5.25e-01 4.63e+01 angle pdb=" N SER N 208 " pdb=" CA SER N 208 " pdb=" C SER N 208 " ideal model delta sigma weight residual 114.31 106.60 7.71 1.29e+00 6.01e-01 3.57e+01 angle pdb=" C3 NAG B 1 " pdb=" C4 NAG B 1 " pdb=" C5 NAG B 1 " ideal model delta sigma weight residual 109.38 119.48 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C GLY A 551 " pdb=" N CYS A 552 " pdb=" CA CYS A 552 " ideal model delta sigma weight residual 122.32 116.42 5.90 1.76e+00 3.23e-01 1.12e+01 angle pdb=" CA PRO A 545 " pdb=" N PRO A 545 " pdb=" CD PRO A 545 " ideal model delta sigma weight residual 112.00 107.35 4.65 1.40e+00 5.10e-01 1.10e+01 ... (remaining 23534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.35: 5977 24.35 - 48.69: 426 48.69 - 73.04: 128 73.04 - 97.38: 52 97.38 - 121.73: 28 Dihedral angle restraints: 6611 sinusoidal: 3619 harmonic: 2992 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 157.88 -64.88 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 486 " pdb=" CB CYS A 486 " ideal model delta sinusoidal sigma weight residual -86.00 -139.91 53.91 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CA PHE A 465 " pdb=" C PHE A 465 " pdb=" N ALA A 466 " pdb=" CA ALA A 466 " ideal model delta harmonic sigma weight residual 180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 6608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 1099 0.273 - 0.545: 4 0.545 - 0.817: 1 0.817 - 1.090: 0 1.090 - 1.362: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" C1 BMA B 5 " pdb=" O6 BMA B 3 " pdb=" C2 BMA B 5 " pdb=" O5 BMA B 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-02 2.50e+03 4.64e+03 chirality pdb=" C1 BMA B 4 " pdb=" O3 BMA B 3 " pdb=" C2 BMA B 4 " pdb=" O5 BMA B 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.60e+02 ... (remaining 1102 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN N 209 " -0.315 2.00e-02 2.50e+03 3.93e-01 2.32e+03 pdb=" CG ASN N 209 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN N 209 " 0.305 2.00e-02 2.50e+03 pdb=" ND2 ASN N 209 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN N 209 " 0.598 2.00e-02 2.50e+03 pdb="HD22 ASN N 209 " -0.614 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 204 " -0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ASN N 204 " 0.084 2.00e-02 2.50e+03 pdb=" O ASN N 204 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS N 205 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 487 " 0.010 2.00e-02 2.50e+03 2.37e-02 2.24e+01 pdb=" CG TRP A 487 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 487 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 487 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 487 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 487 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 487 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 487 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 487 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 487 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 487 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 TRP A 487 " -0.026 2.00e-02 2.50e+03 pdb=" HE3 TRP A 487 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 487 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 487 " -0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP A 487 " 0.026 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 363 2.06 - 2.70: 18380 2.70 - 3.33: 33059 3.33 - 3.97: 44690 3.97 - 4.60: 65605 Nonbonded interactions: 162097 Sorted by model distance: nonbonded pdb=" OE1 GLN M 165 " pdb=" H GLN M 165 " model vdw 1.431 2.450 nonbonded pdb=" HH TYR A 594 " pdb=" O GLY A 600 " model vdw 1.511 2.450 nonbonded pdb="HD11 LEU F 134 " pdb="HG21 VAL N 186 " model vdw 1.554 2.440 nonbonded pdb="HE22 GLN F 123 " pdb=" OG SER F 130 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLN E 39 " pdb="HE22 GLN F 37 " model vdw 1.588 2.450 ... (remaining 162092 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 'C' selection = chain 'D' } 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 group one per residue 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: 2.340 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.005 0.096 6968 Z= 0.251 Angle : 0.877 11.598 9557 Z= 0.397 Chirality : 0.071 1.362 1105 Planarity : 0.006 0.093 1209 Dihedral : 23.721 121.727 2639 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.14 % Allowed : 22.04 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.29), residues: 871 helix: -1.82 (0.87), residues: 37 sheet: 1.14 (0.31), residues: 302 loop : -1.50 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 141 TYR 0.009 0.001 TYR E 106 PHE 0.013 0.001 PHE A 465 TRP 0.048 0.002 TRP A 487 HIS 0.016 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 6940) covalent geometry : angle 0.82101 ( 9487) SS BOND : bond 0.00299 ( 14) SS BOND : angle 0.96573 ( 28) hydrogen bonds : bond 0.25858 ( 216) hydrogen bonds : angle 9.47917 ( 582) link_BETA1-3 : bond 0.01990 ( 1) link_BETA1-3 : angle 7.00856 ( 3) link_BETA1-4 : bond 0.01934 ( 6) link_BETA1-4 : angle 4.00263 ( 18) link_BETA1-6 : bond 0.02167 ( 1) link_BETA1-6 : angle 8.99627 ( 3) link_NAG-ASN : bond 0.01916 ( 6) link_NAG-ASN : angle 3.78087 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1705 time to fit residues: 25.9088 Evaluate side-chains 106 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.165838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133774 restraints weight = 31669.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139011 restraints weight = 17989.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142572 restraints weight = 12466.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144908 restraints weight = 9702.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146337 restraints weight = 8141.827| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6968 Z= 0.170 Angle : 0.797 9.743 9557 Z= 0.374 Chirality : 0.050 0.269 1105 Planarity : 0.006 0.068 1209 Dihedral : 22.817 115.398 1233 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 1.81 % Allowed : 21.20 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.29), residues: 871 helix: -2.59 (0.71), residues: 38 sheet: 1.00 (0.30), residues: 321 loop : -1.45 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 60 TYR 0.009 0.001 TYR F 172 PHE 0.011 0.002 PHE F 97 TRP 0.016 0.001 TRP A 487 HIS 0.007 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6940) covalent geometry : angle 0.76516 ( 9487) SS BOND : bond 0.00379 ( 14) SS BOND : angle 1.29984 ( 28) hydrogen bonds : bond 0.05937 ( 216) hydrogen bonds : angle 7.33053 ( 582) link_BETA1-3 : bond 0.01973 ( 1) link_BETA1-3 : angle 3.01861 ( 3) link_BETA1-4 : bond 0.00531 ( 6) link_BETA1-4 : angle 3.56533 ( 18) link_BETA1-6 : bond 0.01687 ( 1) link_BETA1-6 : angle 6.16691 ( 3) link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.27942 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 424 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7004 (ttp80) REVERT: A 626 ILE cc_start: 0.9256 (mm) cc_final: 0.9041 (mt) REVERT: E 81 MET cc_start: 0.8737 (ttp) cc_final: 0.8439 (ttp) REVERT: F 91 ASP cc_start: 0.7762 (t0) cc_final: 0.7520 (t0) REVERT: F 104 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8279 (p) REVERT: F 146 GLN cc_start: 0.7702 (tp-100) cc_final: 0.6963 (mt0) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 0.1994 time to fit residues: 31.9906 Evaluate side-chains 113 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131578 restraints weight = 32054.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137035 restraints weight = 17610.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140761 restraints weight = 12017.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143149 restraints weight = 9247.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144753 restraints weight = 7764.673| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6968 Z= 0.160 Angle : 0.748 9.705 9557 Z= 0.352 Chirality : 0.049 0.260 1105 Planarity : 0.005 0.058 1209 Dihedral : 18.971 111.793 1233 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.18 % Favored : 90.70 % Rotamer: Outliers : 1.95 % Allowed : 20.78 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 871 helix: -2.03 (0.78), residues: 32 sheet: 1.03 (0.29), residues: 317 loop : -1.46 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.020 0.001 TYR E 105 PHE 0.014 0.001 PHE A 465 TRP 0.013 0.001 TRP A 487 HIS 0.009 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6940) covalent geometry : angle 0.72305 ( 9487) SS BOND : bond 0.00409 ( 14) SS BOND : angle 1.32559 ( 28) hydrogen bonds : bond 0.04568 ( 216) hydrogen bonds : angle 6.59531 ( 582) link_BETA1-3 : bond 0.01132 ( 1) link_BETA1-3 : angle 3.82936 ( 3) link_BETA1-4 : bond 0.00770 ( 6) link_BETA1-4 : angle 2.81879 ( 18) link_BETA1-6 : bond 0.02598 ( 1) link_BETA1-6 : angle 5.29463 ( 3) link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 1.99160 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7122 (ttp80) REVERT: E 81 MET cc_start: 0.8764 (ttp) cc_final: 0.8528 (ttp) REVERT: E 106 TYR cc_start: 0.8314 (m-80) cc_final: 0.7694 (m-80) REVERT: F 82 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: F 91 ASP cc_start: 0.7776 (t0) cc_final: 0.7546 (t0) REVERT: F 146 GLN cc_start: 0.7620 (tp-100) cc_final: 0.6995 (mt0) REVERT: N 206 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7919 (tmmt) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.1739 time to fit residues: 28.5033 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131694 restraints weight = 31596.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137096 restraints weight = 17329.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140788 restraints weight = 11814.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143195 restraints weight = 9096.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144805 restraints weight = 7572.372| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6968 Z= 0.136 Angle : 0.716 9.375 9557 Z= 0.336 Chirality : 0.048 0.282 1105 Planarity : 0.005 0.069 1209 Dihedral : 16.990 113.809 1233 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.07 % Favored : 90.82 % Rotamer: Outliers : 2.65 % Allowed : 21.06 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.28), residues: 871 helix: -1.88 (0.80), residues: 32 sheet: 1.09 (0.29), residues: 312 loop : -1.34 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 483 TYR 0.010 0.001 TYR F 172 PHE 0.014 0.001 PHE A 509 TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6940) covalent geometry : angle 0.69163 ( 9487) SS BOND : bond 0.00390 ( 14) SS BOND : angle 1.20530 ( 28) hydrogen bonds : bond 0.03782 ( 216) hydrogen bonds : angle 6.23439 ( 582) link_BETA1-3 : bond 0.00602 ( 1) link_BETA1-3 : angle 4.11217 ( 3) link_BETA1-4 : bond 0.00595 ( 6) link_BETA1-4 : angle 2.70023 ( 18) link_BETA1-6 : bond 0.02842 ( 1) link_BETA1-6 : angle 4.48338 ( 3) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.08212 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7190 (ttp80) REVERT: A 487 TRP cc_start: 0.8155 (p-90) cc_final: 0.7763 (p-90) REVERT: E 81 MET cc_start: 0.8730 (ttp) cc_final: 0.8518 (ttp) REVERT: F 82 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: F 91 ASP cc_start: 0.7763 (t0) cc_final: 0.7491 (t0) REVERT: F 146 GLN cc_start: 0.7819 (tp-100) cc_final: 0.6977 (mt0) outliers start: 19 outliers final: 13 residues processed: 129 average time/residue: 0.1764 time to fit residues: 30.6424 Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.159317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126186 restraints weight = 32171.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131508 restraints weight = 17627.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135072 restraints weight = 12040.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137452 restraints weight = 9316.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139106 restraints weight = 7801.850| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6968 Z= 0.204 Angle : 0.757 9.549 9557 Z= 0.358 Chirality : 0.048 0.293 1105 Planarity : 0.005 0.059 1209 Dihedral : 15.733 116.413 1229 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.56 % Favored : 89.32 % Rotamer: Outliers : 2.93 % Allowed : 19.94 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.28), residues: 871 helix: -1.64 (0.94), residues: 26 sheet: 0.94 (0.30), residues: 311 loop : -1.42 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 141 TYR 0.015 0.002 TYR E 106 PHE 0.016 0.002 PHE A 465 TRP 0.009 0.001 TRP A 487 HIS 0.009 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6940) covalent geometry : angle 0.73436 ( 9487) SS BOND : bond 0.00462 ( 14) SS BOND : angle 1.42228 ( 28) hydrogen bonds : bond 0.03947 ( 216) hydrogen bonds : angle 6.19771 ( 582) link_BETA1-3 : bond 0.01066 ( 1) link_BETA1-3 : angle 3.52560 ( 3) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 2.70256 ( 18) link_BETA1-6 : bond 0.02451 ( 1) link_BETA1-6 : angle 3.73240 ( 3) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.32681 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 487 TRP cc_start: 0.8003 (p-90) cc_final: 0.7563 (p-90) REVERT: F 26 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8365 (ttmm) REVERT: F 82 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: F 91 ASP cc_start: 0.7840 (t0) cc_final: 0.7514 (t0) REVERT: F 146 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7034 (mt0) outliers start: 21 outliers final: 19 residues processed: 130 average time/residue: 0.1603 time to fit residues: 28.5777 Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 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 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127333 restraints weight = 31757.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132742 restraints weight = 17081.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136408 restraints weight = 11576.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138788 restraints weight = 8880.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140322 restraints weight = 7414.001| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6968 Z= 0.147 Angle : 0.724 10.348 9557 Z= 0.341 Chirality : 0.047 0.285 1105 Planarity : 0.005 0.072 1209 Dihedral : 15.022 115.877 1229 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.41 % Favored : 90.47 % Rotamer: Outliers : 2.93 % Allowed : 21.20 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.29), residues: 871 helix: -2.29 (0.84), residues: 32 sheet: 1.01 (0.30), residues: 309 loop : -1.33 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.011 0.001 TYR E 106 PHE 0.011 0.002 PHE A 509 TRP 0.009 0.001 TRP A 487 HIS 0.007 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6940) covalent geometry : angle 0.70146 ( 9487) SS BOND : bond 0.00389 ( 14) SS BOND : angle 1.26405 ( 28) hydrogen bonds : bond 0.03474 ( 216) hydrogen bonds : angle 6.03566 ( 582) link_BETA1-3 : bond 0.00705 ( 1) link_BETA1-3 : angle 3.49880 ( 3) link_BETA1-4 : bond 0.00569 ( 6) link_BETA1-4 : angle 2.55285 ( 18) link_BETA1-6 : bond 0.02475 ( 1) link_BETA1-6 : angle 3.68946 ( 3) link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 2.37530 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7396 (ttp80) REVERT: A 487 TRP cc_start: 0.8021 (p-90) cc_final: 0.7653 (p-90) REVERT: A 562 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6793 (mmtp) REVERT: A 589 HIS cc_start: 0.7729 (t70) cc_final: 0.7481 (t-90) REVERT: F 82 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: F 91 ASP cc_start: 0.7852 (t0) cc_final: 0.7536 (t0) REVERT: F 146 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7006 (mt0) outliers start: 21 outliers final: 18 residues processed: 123 average time/residue: 0.1634 time to fit residues: 27.1730 Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128536 restraints weight = 31994.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134106 restraints weight = 17240.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137762 restraints weight = 11635.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140223 restraints weight = 8953.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141882 restraints weight = 7458.688| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6968 Z= 0.120 Angle : 0.690 9.495 9557 Z= 0.325 Chirality : 0.046 0.195 1105 Planarity : 0.005 0.072 1209 Dihedral : 13.509 114.780 1229 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.96 % Favored : 90.93 % Rotamer: Outliers : 3.21 % Allowed : 20.92 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.29), residues: 871 helix: -1.38 (0.94), residues: 26 sheet: 1.07 (0.30), residues: 309 loop : -1.24 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.037 0.001 TYR E 108 PHE 0.052 0.002 PHE A 465 TRP 0.010 0.001 TRP A 487 HIS 0.005 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6940) covalent geometry : angle 0.66409 ( 9487) SS BOND : bond 0.00350 ( 14) SS BOND : angle 1.16129 ( 28) hydrogen bonds : bond 0.03144 ( 216) hydrogen bonds : angle 5.82422 ( 582) link_BETA1-3 : bond 0.00549 ( 1) link_BETA1-3 : angle 3.25579 ( 3) link_BETA1-4 : bond 0.00562 ( 6) link_BETA1-4 : angle 2.48253 ( 18) link_BETA1-6 : bond 0.02433 ( 1) link_BETA1-6 : angle 3.67523 ( 3) link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 2.88612 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7356 (ttp80) REVERT: A 487 TRP cc_start: 0.7989 (p-90) cc_final: 0.7534 (p-90) REVERT: A 557 SER cc_start: 0.7905 (p) cc_final: 0.7667 (m) REVERT: A 562 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6724 (mmtp) REVERT: F 82 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: F 91 ASP cc_start: 0.7815 (t0) cc_final: 0.7514 (t0) REVERT: F 146 GLN cc_start: 0.7739 (tp-100) cc_final: 0.6928 (mt0) outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.1754 time to fit residues: 29.9443 Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125975 restraints weight = 32016.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131428 restraints weight = 17456.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135035 restraints weight = 11863.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137514 restraints weight = 9189.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139177 restraints weight = 7643.099| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6968 Z= 0.181 Angle : 0.710 9.460 9557 Z= 0.340 Chirality : 0.046 0.197 1105 Planarity : 0.005 0.068 1209 Dihedral : 13.089 115.636 1229 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.22 % Favored : 89.67 % Rotamer: Outliers : 2.93 % Allowed : 21.48 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.29), residues: 871 helix: -1.49 (0.97), residues: 26 sheet: 1.02 (0.30), residues: 309 loop : -1.32 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.013 0.001 TYR E 106 PHE 0.014 0.002 PHE A 465 TRP 0.008 0.001 TRP A 487 HIS 0.006 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6940) covalent geometry : angle 0.68370 ( 9487) SS BOND : bond 0.00419 ( 14) SS BOND : angle 1.31062 ( 28) hydrogen bonds : bond 0.03448 ( 216) hydrogen bonds : angle 5.84702 ( 582) link_BETA1-3 : bond 0.00713 ( 1) link_BETA1-3 : angle 2.67443 ( 3) link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 2.36716 ( 18) link_BETA1-6 : bond 0.02153 ( 1) link_BETA1-6 : angle 3.62812 ( 3) link_NAG-ASN : bond 0.00102 ( 6) link_NAG-ASN : angle 3.16148 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7468 (ttp80) REVERT: A 487 TRP cc_start: 0.8002 (p-90) cc_final: 0.7481 (p-90) REVERT: A 557 SER cc_start: 0.8029 (p) cc_final: 0.7796 (m) REVERT: A 562 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6919 (mmtp) REVERT: F 82 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: F 91 ASP cc_start: 0.7824 (t0) cc_final: 0.7508 (t0) REVERT: F 146 GLN cc_start: 0.7813 (tp-100) cc_final: 0.6957 (mt0) outliers start: 21 outliers final: 18 residues processed: 125 average time/residue: 0.1846 time to fit residues: 30.8668 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127998 restraints weight = 32040.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133543 restraints weight = 17200.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137226 restraints weight = 11605.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139519 restraints weight = 8922.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141254 restraints weight = 7484.915| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6968 Z= 0.122 Angle : 0.680 8.540 9557 Z= 0.327 Chirality : 0.046 0.211 1105 Planarity : 0.005 0.066 1209 Dihedral : 12.609 114.334 1229 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 2.79 % Allowed : 21.90 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.29), residues: 871 helix: -1.42 (0.95), residues: 26 sheet: 1.05 (0.30), residues: 311 loop : -1.21 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.016 0.001 TYR E 108 PHE 0.027 0.001 PHE A 465 TRP 0.010 0.001 TRP A 487 HIS 0.002 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6940) covalent geometry : angle 0.65539 ( 9487) SS BOND : bond 0.00357 ( 14) SS BOND : angle 1.17536 ( 28) hydrogen bonds : bond 0.03066 ( 216) hydrogen bonds : angle 5.68866 ( 582) link_BETA1-3 : bond 0.00552 ( 1) link_BETA1-3 : angle 2.39846 ( 3) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.24865 ( 18) link_BETA1-6 : bond 0.02211 ( 1) link_BETA1-6 : angle 3.59559 ( 3) link_NAG-ASN : bond 0.00215 ( 6) link_NAG-ASN : angle 2.96806 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7388 (ttp80) REVERT: A 487 TRP cc_start: 0.7972 (p-90) cc_final: 0.7487 (p-90) REVERT: A 557 SER cc_start: 0.8003 (p) cc_final: 0.7782 (m) REVERT: A 562 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6811 (mmtp) REVERT: F 82 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: F 91 ASP cc_start: 0.7837 (t0) cc_final: 0.7546 (t0) REVERT: F 146 GLN cc_start: 0.7755 (tp-100) cc_final: 0.6947 (mt0) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.1836 time to fit residues: 29.9490 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127377 restraints weight = 31923.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132846 restraints weight = 17195.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136517 restraints weight = 11628.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138926 restraints weight = 8941.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140523 restraints weight = 7461.520| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6968 Z= 0.135 Angle : 0.684 8.502 9557 Z= 0.328 Chirality : 0.045 0.215 1105 Planarity : 0.004 0.065 1209 Dihedral : 12.307 113.965 1229 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.53 % Favored : 90.36 % Rotamer: Outliers : 2.79 % Allowed : 21.90 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.29), residues: 871 helix: -1.30 (0.97), residues: 26 sheet: 1.04 (0.30), residues: 311 loop : -1.21 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.011 0.001 TYR A 611 PHE 0.032 0.002 PHE A 465 TRP 0.020 0.001 TRP A 469 HIS 0.003 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6940) covalent geometry : angle 0.66053 ( 9487) SS BOND : bond 0.00369 ( 14) SS BOND : angle 1.21784 ( 28) hydrogen bonds : bond 0.03052 ( 216) hydrogen bonds : angle 5.62597 ( 582) link_BETA1-3 : bond 0.00711 ( 1) link_BETA1-3 : angle 1.91430 ( 3) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 2.20179 ( 18) link_BETA1-6 : bond 0.01811 ( 1) link_BETA1-6 : angle 3.58216 ( 3) link_NAG-ASN : bond 0.00170 ( 6) link_NAG-ASN : angle 2.94220 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7390 (ttp80) REVERT: A 487 TRP cc_start: 0.7997 (p-90) cc_final: 0.7537 (p-90) REVERT: A 557 SER cc_start: 0.8025 (p) cc_final: 0.7816 (m) REVERT: A 562 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6841 (mmtp) REVERT: F 82 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: F 91 ASP cc_start: 0.7795 (t0) cc_final: 0.7537 (t0) REVERT: F 146 GLN cc_start: 0.7786 (tp-100) cc_final: 0.6975 (mt0) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.1813 time to fit residues: 29.6080 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127111 restraints weight = 32170.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132644 restraints weight = 17282.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136307 restraints weight = 11656.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138707 restraints weight = 8963.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140396 restraints weight = 7504.808| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6968 Z= 0.136 Angle : 0.682 8.440 9557 Z= 0.329 Chirality : 0.045 0.222 1105 Planarity : 0.005 0.065 1209 Dihedral : 12.113 113.608 1229 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 2.93 % Allowed : 22.32 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.29), residues: 871 helix: -1.34 (0.97), residues: 26 sheet: 1.06 (0.30), residues: 311 loop : -1.20 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 639 TYR 0.012 0.001 TYR E 108 PHE 0.014 0.001 PHE A 465 TRP 0.016 0.001 TRP A 469 HIS 0.003 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6940) covalent geometry : angle 0.65809 ( 9487) SS BOND : bond 0.00365 ( 14) SS BOND : angle 1.21725 ( 28) hydrogen bonds : bond 0.03042 ( 216) hydrogen bonds : angle 5.55719 ( 582) link_BETA1-3 : bond 0.00651 ( 1) link_BETA1-3 : angle 1.83252 ( 3) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 2.19287 ( 18) link_BETA1-6 : bond 0.01982 ( 1) link_BETA1-6 : angle 3.73642 ( 3) link_NAG-ASN : bond 0.00195 ( 6) link_NAG-ASN : angle 2.94884 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.13 seconds wall clock time: 44 minutes 29.96 seconds (2669.96 seconds total)