Starting phenix.real_space_refine on Thu May 15 11:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u9y_42041/05_2025/8u9y_42041_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u9y_42041/05_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_42041/05_2025/8u9y_42041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u9y_42041/05_2025/8u9y_42041.map" model { file = "/net/cci-nas-00/data/ceres_data/8u9y_42041/05_2025/8u9y_42041_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u9y_42041/05_2025/8u9y_42041_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 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, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 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: 7.26, per 1000 atoms: 0.56 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: 3.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.15 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: 4.32 Time building geometry restraints manager: 3.94 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: 4.060 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: 0.250 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (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 TRP 0.048 0.002 TRP A 487 HIS 0.016 0.001 HIS A 589 PHE 0.013 0.001 PHE A 465 TYR 0.009 0.001 TYR E 106 ARG 0.005 0.001 ARG M 141 Details of bonding type rmsd link_NAG-ASN : bond 0.01916 ( 6) link_NAG-ASN : angle 3.78087 ( 18) link_BETA1-4 : bond 0.01934 ( 6) link_BETA1-4 : angle 4.00263 ( 18) hydrogen bonds : bond 0.25858 ( 216) hydrogen bonds : angle 9.47917 ( 582) link_BETA1-6 : bond 0.02167 ( 1) link_BETA1-6 : angle 8.99627 ( 3) SS BOND : bond 0.00299 ( 14) SS BOND : angle 0.96573 ( 28) link_BETA1-3 : bond 0.01990 ( 1) link_BETA1-3 : angle 7.00856 ( 3) covalent geometry : bond 0.00506 ( 6940) covalent geometry : angle 0.82101 ( 9487) *********************** 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 : 0.987 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: 0.3546 time to fit residues: 54.1223 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 : 1.022 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133540 restraints weight = 31527.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138995 restraints weight = 17465.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142700 restraints weight = 11965.195| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1127 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 : 0.801 10.016 9557 Z= 0.374 Chirality : 0.051 0.266 1105 Planarity : 0.006 0.065 1209 Dihedral : 22.116 117.701 1233 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 1.81 % Allowed : 21.34 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.29), residues: 871 helix: -2.62 (0.70), residues: 38 sheet: 0.99 (0.29), residues: 321 loop : -1.44 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 487 HIS 0.007 0.001 HIS A 589 PHE 0.012 0.002 PHE F 97 TYR 0.010 0.001 TYR F 172 ARG 0.002 0.000 ARG F 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 2.19513 ( 18) link_BETA1-4 : bond 0.00527 ( 6) link_BETA1-4 : angle 3.67923 ( 18) hydrogen bonds : bond 0.04784 ( 216) hydrogen bonds : angle 7.17327 ( 582) link_BETA1-6 : bond 0.01649 ( 1) link_BETA1-6 : angle 5.86565 ( 3) SS BOND : bond 0.00440 ( 14) SS BOND : angle 1.41104 ( 28) link_BETA1-3 : bond 0.00586 ( 1) link_BETA1-3 : angle 3.11027 ( 3) covalent geometry : bond 0.00378 ( 6940) covalent geometry : angle 0.76938 ( 9487) *********************** 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 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.952 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: "HIS A 653 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 424 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6926 (ttp80) REVERT: A 626 ILE cc_start: 0.9231 (mm) cc_final: 0.9024 (mt) REVERT: E 81 MET cc_start: 0.8791 (ttp) cc_final: 0.8507 (ttp) REVERT: F 91 ASP cc_start: 0.7731 (t0) cc_final: 0.7508 (t0) REVERT: F 104 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8056 (p) REVERT: F 146 GLN cc_start: 0.7691 (tp-100) cc_final: 0.6921 (mt0) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.3789 time to fit residues: 62.1126 Evaluate side-chains 119 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.165215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132640 restraints weight = 31712.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138076 restraints weight = 17475.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141737 restraints weight = 11943.866| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6968 Z= 0.147 Angle : 0.741 9.580 9557 Z= 0.347 Chirality : 0.049 0.262 1105 Planarity : 0.005 0.059 1209 Dihedral : 18.855 111.055 1233 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.84 % Favored : 91.04 % Rotamer: Outliers : 1.95 % Allowed : 20.50 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 871 helix: -2.02 (0.79), residues: 32 sheet: 1.13 (0.29), residues: 316 loop : -1.41 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.011 0.001 HIS A 589 PHE 0.013 0.001 PHE A 465 TYR 0.010 0.001 TYR F 172 ARG 0.001 0.000 ARG E 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 6) link_NAG-ASN : angle 1.96818 ( 18) link_BETA1-4 : bond 0.00627 ( 6) link_BETA1-4 : angle 2.81236 ( 18) hydrogen bonds : bond 0.04290 ( 216) hydrogen bonds : angle 6.58659 ( 582) link_BETA1-6 : bond 0.02725 ( 1) link_BETA1-6 : angle 5.17415 ( 3) SS BOND : bond 0.00482 ( 14) SS BOND : angle 1.34380 ( 28) link_BETA1-3 : bond 0.00967 ( 1) link_BETA1-3 : angle 3.79106 ( 3) covalent geometry : bond 0.00341 ( 6940) covalent geometry : angle 0.71627 ( 9487) *********************** 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 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.963 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: "HIS A 653 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7021 (ttp80) REVERT: E 81 MET cc_start: 0.8805 (ttp) cc_final: 0.8574 (ttp) REVERT: F 82 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: F 91 ASP cc_start: 0.7750 (t0) cc_final: 0.7490 (t0) REVERT: F 146 GLN cc_start: 0.7642 (tp-100) cc_final: 0.6973 (mt0) REVERT: N 153 GLU cc_start: 0.8029 (pm20) cc_final: 0.7750 (pp20) REVERT: N 206 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7909 (tmmt) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.3753 time to fit residues: 62.8892 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 : 1.042 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130366 restraints weight = 31747.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135751 restraints weight = 17680.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139422 restraints weight = 12198.969| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1798 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= 0.144 Angle : 0.716 9.048 9557 Z= 0.337 Chirality : 0.048 0.284 1105 Planarity : 0.005 0.076 1209 Dihedral : 16.690 114.634 1233 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.53 % Favored : 90.36 % Rotamer: Outliers : 2.93 % Allowed : 20.50 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 871 helix: -1.82 (0.81), residues: 32 sheet: 1.10 (0.30), residues: 312 loop : -1.30 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.007 0.001 HIS A 589 PHE 0.015 0.001 PHE A 465 TYR 0.010 0.001 TYR E 106 ARG 0.002 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 2.13999 ( 18) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.72578 ( 18) hydrogen bonds : bond 0.03712 ( 216) hydrogen bonds : angle 6.17617 ( 582) link_BETA1-6 : bond 0.02677 ( 1) link_BETA1-6 : angle 4.16369 ( 3) SS BOND : bond 0.00380 ( 14) SS BOND : angle 1.23148 ( 28) link_BETA1-3 : bond 0.00552 ( 1) link_BETA1-3 : angle 3.93935 ( 3) covalent geometry : bond 0.00339 ( 6940) covalent geometry : angle 0.69220 ( 9487) *********************** 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 138 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.103 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 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7153 (ttp80) REVERT: A 487 TRP cc_start: 0.8181 (p-90) cc_final: 0.7733 (p-90) REVERT: E 81 MET cc_start: 0.8804 (ttp) cc_final: 0.8596 (ttp) REVERT: F 82 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: F 91 ASP cc_start: 0.7772 (t0) cc_final: 0.7512 (t0) REVERT: N 153 GLU cc_start: 0.7975 (pm20) cc_final: 0.7657 (pp20) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.3620 time to fit residues: 63.7684 Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.161019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127663 restraints weight = 32402.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133099 restraints weight = 17600.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136790 restraints weight = 11967.115| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6968 Z= 0.168 Angle : 0.726 9.602 9557 Z= 0.341 Chirality : 0.048 0.299 1105 Planarity : 0.005 0.067 1209 Dihedral : 15.510 114.989 1229 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.64 % Favored : 90.24 % Rotamer: Outliers : 2.51 % Allowed : 19.94 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 871 helix: -1.47 (0.93), residues: 26 sheet: 1.08 (0.30), residues: 309 loop : -1.31 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.006 0.001 HIS A 617 PHE 0.015 0.002 PHE A 465 TYR 0.027 0.002 TYR E 105 ARG 0.004 0.000 ARG M 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 6) link_NAG-ASN : angle 2.18770 ( 18) link_BETA1-4 : bond 0.00588 ( 6) link_BETA1-4 : angle 2.66132 ( 18) hydrogen bonds : bond 0.03662 ( 216) hydrogen bonds : angle 6.04390 ( 582) link_BETA1-6 : bond 0.02371 ( 1) link_BETA1-6 : angle 3.68888 ( 3) SS BOND : bond 0.00399 ( 14) SS BOND : angle 1.25421 ( 28) link_BETA1-3 : bond 0.00853 ( 1) link_BETA1-3 : angle 3.60831 ( 3) covalent geometry : bond 0.00398 ( 6940) covalent geometry : angle 0.70332 ( 9487) *********************** 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 131 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.088 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: 0.8168 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: A 487 TRP cc_start: 0.8099 (p-90) cc_final: 0.7620 (p-90) REVERT: E 202 ASN cc_start: 0.7872 (t0) cc_final: 0.7624 (t0) REVERT: F 82 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: F 91 ASP cc_start: 0.7822 (t0) cc_final: 0.7531 (t0) outliers start: 18 outliers final: 16 residues processed: 126 average time/residue: 0.3733 time to fit residues: 63.4351 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 : 0.965 ------------------------------------------------------------------------------- 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 564 CYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127554 restraints weight = 32508.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133066 restraints weight = 17512.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136737 restraints weight = 11847.962| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6968 Z= 0.151 Angle : 0.715 10.569 9557 Z= 0.336 Chirality : 0.047 0.257 1105 Planarity : 0.005 0.069 1209 Dihedral : 14.612 115.609 1229 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.18 % Favored : 90.70 % Rotamer: Outliers : 3.07 % Allowed : 20.64 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 871 helix: -2.25 (0.82), residues: 32 sheet: 1.08 (0.30), residues: 309 loop : -1.30 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 487 HIS 0.005 0.001 HIS A 617 PHE 0.010 0.001 PHE A 509 TYR 0.017 0.001 TYR E 105 ARG 0.003 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 6) link_NAG-ASN : angle 2.42176 ( 18) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 2.55354 ( 18) hydrogen bonds : bond 0.03396 ( 216) hydrogen bonds : angle 5.88578 ( 582) link_BETA1-6 : bond 0.02384 ( 1) link_BETA1-6 : angle 3.64908 ( 3) SS BOND : bond 0.00386 ( 14) SS BOND : angle 1.21880 ( 28) link_BETA1-3 : bond 0.00692 ( 1) link_BETA1-3 : angle 3.36040 ( 3) covalent geometry : bond 0.00362 ( 6940) covalent geometry : angle 0.69189 ( 9487) *********************** 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 131 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.033 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 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: 0.8200 (OUTLIER) cc_final: 0.7284 (ttp80) REVERT: A 487 TRP cc_start: 0.8042 (p-90) cc_final: 0.7519 (p-90) REVERT: A 562 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6838 (mmtp) REVERT: E 202 ASN cc_start: 0.7802 (t0) cc_final: 0.7563 (t0) REVERT: F 82 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: F 91 ASP cc_start: 0.7883 (t0) cc_final: 0.7561 (t0) REVERT: F 146 GLN cc_start: 0.7870 (tp-100) cc_final: 0.6958 (mt0) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.3616 time to fit residues: 60.2040 Evaluate side-chains 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 562 LYS Chi-restraints excluded: chain A residue 564 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN N 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126239 restraints weight = 32157.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131666 restraints weight = 17469.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135260 restraints weight = 11885.584| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2623 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= 0.175 Angle : 0.716 9.777 9557 Z= 0.340 Chirality : 0.046 0.193 1105 Planarity : 0.005 0.063 1209 Dihedral : 13.599 115.718 1229 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.45 % Favored : 89.44 % Rotamer: Outliers : 3.49 % Allowed : 20.78 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.29), residues: 871 helix: -2.29 (0.84), residues: 32 sheet: 1.05 (0.30), residues: 309 loop : -1.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.005 0.001 HIS A 617 PHE 0.014 0.002 PHE A 550 TYR 0.013 0.001 TYR E 106 ARG 0.003 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 6) link_NAG-ASN : angle 3.02220 ( 18) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.48199 ( 18) hydrogen bonds : bond 0.03469 ( 216) hydrogen bonds : angle 5.86641 ( 582) link_BETA1-6 : bond 0.02346 ( 1) link_BETA1-6 : angle 3.63517 ( 3) SS BOND : bond 0.00404 ( 14) SS BOND : angle 1.27923 ( 28) link_BETA1-3 : bond 0.00819 ( 1) link_BETA1-3 : angle 3.09828 ( 3) covalent geometry : bond 0.00415 ( 6940) covalent geometry : angle 0.68926 ( 9487) *********************** 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 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.327 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: 0.8329 (OUTLIER) cc_final: 0.7444 (ttp80) REVERT: A 487 TRP cc_start: 0.8020 (p-90) cc_final: 0.7521 (p-90) REVERT: A 562 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6990 (mmtp) REVERT: E 202 ASN cc_start: 0.7879 (t0) cc_final: 0.7622 (t0) REVERT: F 82 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: F 91 ASP cc_start: 0.7890 (t0) cc_final: 0.7578 (t0) REVERT: F 146 GLN cc_start: 0.7836 (tp-100) cc_final: 0.6999 (mt0) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.3629 time to fit residues: 61.7136 Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 606 ARG 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 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 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.160626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127644 restraints weight = 31865.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133143 restraints weight = 17113.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136840 restraints weight = 11527.615| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6968 Z= 0.139 Angle : 0.691 9.213 9557 Z= 0.329 Chirality : 0.046 0.204 1105 Planarity : 0.005 0.066 1209 Dihedral : 12.901 114.913 1229 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 2.79 % Allowed : 21.20 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.29), residues: 871 helix: -2.28 (0.83), residues: 32 sheet: 1.10 (0.30), residues: 309 loop : -1.27 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.003 0.001 HIS A 617 PHE 0.044 0.002 PHE A 465 TYR 0.014 0.001 TYR E 105 ARG 0.002 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 6) link_NAG-ASN : angle 3.12601 ( 18) link_BETA1-4 : bond 0.00556 ( 6) link_BETA1-4 : angle 2.29192 ( 18) hydrogen bonds : bond 0.03188 ( 216) hydrogen bonds : angle 5.73675 ( 582) link_BETA1-6 : bond 0.02274 ( 1) link_BETA1-6 : angle 3.60105 ( 3) SS BOND : bond 0.00391 ( 14) SS BOND : angle 1.21472 ( 28) link_BETA1-3 : bond 0.00652 ( 1) link_BETA1-3 : angle 2.74199 ( 3) covalent geometry : bond 0.00334 ( 6940) covalent geometry : angle 0.66407 ( 9487) *********************** 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 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.943 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 revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7410 (ttp80) REVERT: A 487 TRP cc_start: 0.8041 (p-90) cc_final: 0.7554 (p-90) REVERT: A 557 SER cc_start: 0.8000 (p) cc_final: 0.7763 (m) REVERT: A 562 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6891 (mmtp) REVERT: E 65 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6576 (mm-40) REVERT: E 89 GLU cc_start: 0.8593 (mp0) cc_final: 0.8061 (mp0) REVERT: E 202 ASN cc_start: 0.7825 (t0) cc_final: 0.7586 (t0) REVERT: F 82 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: F 91 ASP cc_start: 0.7852 (t0) cc_final: 0.7533 (t0) REVERT: F 146 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7012 (mt0) outliers start: 20 outliers final: 16 residues processed: 121 average time/residue: 0.3867 time to fit residues: 62.5072 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 606 ARG 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 N residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 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 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 = 0.3944 r_free = 0.3944 target = 0.159839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126594 restraints weight = 32267.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132012 restraints weight = 17442.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135714 restraints weight = 11840.302| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6968 Z= 0.148 Angle : 0.687 8.567 9557 Z= 0.330 Chirality : 0.046 0.210 1105 Planarity : 0.005 0.059 1209 Dihedral : 12.563 114.637 1229 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.10 % Favored : 89.78 % Rotamer: Outliers : 2.79 % Allowed : 21.48 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 871 helix: -1.42 (0.97), residues: 26 sheet: 1.02 (0.30), residues: 311 loop : -1.26 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.004 0.001 HIS A 617 PHE 0.014 0.001 PHE A 550 TYR 0.012 0.001 TYR E 105 ARG 0.002 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 6) link_NAG-ASN : angle 3.03588 ( 18) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 2.27583 ( 18) hydrogen bonds : bond 0.03211 ( 216) hydrogen bonds : angle 5.67850 ( 582) link_BETA1-6 : bond 0.02186 ( 1) link_BETA1-6 : angle 3.67459 ( 3) SS BOND : bond 0.00381 ( 14) SS BOND : angle 1.25492 ( 28) link_BETA1-3 : bond 0.00717 ( 1) link_BETA1-3 : angle 2.24360 ( 3) covalent geometry : bond 0.00356 ( 6940) covalent geometry : angle 0.66169 ( 9487) *********************** 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 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.007 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: 0.8286 (OUTLIER) cc_final: 0.7377 (ttp80) REVERT: A 487 TRP cc_start: 0.8039 (p-90) cc_final: 0.7498 (p-90) REVERT: A 557 SER cc_start: 0.8052 (p) cc_final: 0.7827 (m) REVERT: A 562 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6827 (mmtp) REVERT: E 65 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6646 (mm-40) REVERT: E 89 GLU cc_start: 0.8613 (mp0) cc_final: 0.8062 (mp0) REVERT: E 202 ASN cc_start: 0.7792 (t0) cc_final: 0.7550 (t0) REVERT: F 82 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: F 91 ASP cc_start: 0.7870 (t0) cc_final: 0.7547 (t0) REVERT: F 146 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7001 (mt0) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.3843 time to fit residues: 62.2488 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 480 SER 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 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 606 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 0.0980 chunk 49 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.161655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128455 restraints weight = 32225.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134044 restraints weight = 17317.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137692 restraints weight = 11688.011| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6968 Z= 0.113 Angle : 0.666 8.275 9557 Z= 0.320 Chirality : 0.045 0.221 1105 Planarity : 0.005 0.061 1209 Dihedral : 12.172 113.304 1229 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.08 % Rotamer: Outliers : 2.37 % Allowed : 21.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 871 helix: -1.01 (1.11), residues: 20 sheet: 1.10 (0.30), residues: 311 loop : -1.17 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 469 HIS 0.002 0.001 HIS N 205 PHE 0.012 0.001 PHE A 509 TYR 0.014 0.001 TYR A 611 ARG 0.006 0.000 ARG A 639 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.90937 ( 18) link_BETA1-4 : bond 0.00560 ( 6) link_BETA1-4 : angle 2.19602 ( 18) hydrogen bonds : bond 0.02930 ( 216) hydrogen bonds : angle 5.52701 ( 582) link_BETA1-6 : bond 0.02091 ( 1) link_BETA1-6 : angle 3.63179 ( 3) SS BOND : bond 0.00339 ( 14) SS BOND : angle 1.13285 ( 28) link_BETA1-3 : bond 0.00533 ( 1) link_BETA1-3 : angle 1.90630 ( 3) covalent geometry : bond 0.00276 ( 6940) covalent geometry : angle 0.64234 ( 9487) ********************** 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 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.109 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: 0.8210 (OUTLIER) cc_final: 0.7276 (ttp80) REVERT: A 487 TRP cc_start: 0.8100 (p-90) cc_final: 0.7592 (p-90) REVERT: A 557 SER cc_start: 0.8046 (p) cc_final: 0.7827 (m) REVERT: A 562 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6794 (mmtp) REVERT: E 65 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6479 (mm-40) REVERT: E 89 GLU cc_start: 0.8600 (mp0) cc_final: 0.8044 (mp0) REVERT: E 202 ASN cc_start: 0.7700 (t0) cc_final: 0.7499 (t0) REVERT: F 82 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: F 91 ASP cc_start: 0.7772 (t0) cc_final: 0.7513 (t0) REVERT: F 141 ARG cc_start: 0.8844 (tpt90) cc_final: 0.8640 (tpt90) REVERT: F 146 GLN cc_start: 0.7780 (tp-100) cc_final: 0.6980 (mt0) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.4120 time to fit residues: 65.2104 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 M residue 149 VAL 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 9 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.160205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126955 restraints weight = 32249.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132468 restraints weight = 17339.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136143 restraints weight = 11726.065| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3105 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= 0.141 Angle : 0.678 8.323 9557 Z= 0.325 Chirality : 0.045 0.221 1105 Planarity : 0.004 0.058 1209 Dihedral : 12.041 113.347 1229 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.87 % Favored : 90.01 % Rotamer: Outliers : 2.51 % Allowed : 22.04 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 871 helix: -1.25 (0.97), residues: 26 sheet: 1.08 (0.30), residues: 311 loop : -1.19 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.004 0.001 HIS A 617 PHE 0.022 0.001 PHE A 465 TYR 0.011 0.001 TYR E 105 ARG 0.002 0.000 ARG A 639 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 6) link_NAG-ASN : angle 2.93640 ( 18) link_BETA1-4 : bond 0.00487 ( 6) link_BETA1-4 : angle 2.18173 ( 18) hydrogen bonds : bond 0.03069 ( 216) hydrogen bonds : angle 5.52655 ( 582) link_BETA1-6 : bond 0.01912 ( 1) link_BETA1-6 : angle 3.79391 ( 3) SS BOND : bond 0.00368 ( 14) SS BOND : angle 1.22053 ( 28) link_BETA1-3 : bond 0.00739 ( 1) link_BETA1-3 : angle 1.77806 ( 3) covalent geometry : bond 0.00342 ( 6940) covalent geometry : angle 0.65379 ( 9487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.41 seconds wall clock time: 77 minutes 38.56 seconds (4658.56 seconds total)