Starting phenix.real_space_refine on Wed Jun 11 17:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u9y_42041/06_2025/8u9y_42041_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u9y_42041/06_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_42041/06_2025/8u9y_42041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u9y_42041/06_2025/8u9y_42041.map" model { file = "/net/cci-nas-00/data/ceres_data/8u9y_42041/06_2025/8u9y_42041_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u9y_42041/06_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-5710/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: 7.93, per 1000 atoms: 0.61 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: 3.55 Conformation dependent library (CDL) restraints added in 1.5 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: 1.44 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: 7.11 Time building geometry restraints manager: 4.28 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: 17.900 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: 0.240 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.790 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- 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 : 1.132 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: 0.3633 time to fit residues: 55.5664 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 : 1.056 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133566 restraints weight = 31527.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138977 restraints weight = 17447.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142616 restraints weight = 11982.149| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 3.67927 ( 18) hydrogen bonds : bond 0.04784 ( 216) hydrogen bonds : angle 7.17327 ( 582) link_BETA1-6 : bond 0.01648 ( 1) link_BETA1-6 : angle 5.86567 ( 3) SS BOND : bond 0.00440 ( 14) SS BOND : angle 1.41104 ( 28) link_BETA1-3 : bond 0.00586 ( 1) link_BETA1-3 : angle 3.10996 ( 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 : 0.978 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: 0.7825 (OUTLIER) cc_final: 0.6925 (ttp80) REVERT: A 626 ILE cc_start: 0.9229 (mm) cc_final: 0.9022 (mt) REVERT: E 81 MET cc_start: 0.8790 (ttp) cc_final: 0.8506 (ttp) REVERT: F 91 ASP cc_start: 0.7730 (t0) cc_final: 0.7506 (t0) REVERT: F 104 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8057 (p) REVERT: F 146 GLN cc_start: 0.7689 (tp-100) cc_final: 0.6919 (mt0) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.3949 time to fit residues: 65.0613 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 : 1.045 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132868 restraints weight = 31729.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138286 restraints weight = 17536.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141884 restraints weight = 11994.499| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1476 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= 0.140 Angle : 0.733 9.560 9557 Z= 0.343 Chirality : 0.049 0.255 1105 Planarity : 0.005 0.058 1209 Dihedral : 18.681 111.192 1233 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.38 % Favored : 91.50 % Rotamer: Outliers : 1.95 % Allowed : 20.36 % Favored : 77.68 % 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: -0.62 (0.28), residues: 871 helix: -1.99 (0.79), residues: 32 sheet: 1.14 (0.29), residues: 316 loop : -1.39 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.010 0.001 HIS A 589 PHE 0.014 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 0.00270 ( 6) link_NAG-ASN : angle 1.96693 ( 18) link_BETA1-4 : bond 0.00806 ( 6) link_BETA1-4 : angle 2.72091 ( 18) hydrogen bonds : bond 0.04305 ( 216) hydrogen bonds : angle 6.53242 ( 582) link_BETA1-6 : bond 0.02693 ( 1) link_BETA1-6 : angle 5.18215 ( 3) SS BOND : bond 0.00384 ( 14) SS BOND : angle 1.24996 ( 28) link_BETA1-3 : bond 0.01198 ( 1) link_BETA1-3 : angle 3.98481 ( 3) covalent geometry : bond 0.00322 ( 6940) covalent geometry : angle 0.70867 ( 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 : 0.983 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7000 (ttp80) REVERT: E 81 MET cc_start: 0.8800 (ttp) cc_final: 0.8570 (ttp) REVERT: F 82 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: F 146 GLN cc_start: 0.7630 (tp-100) cc_final: 0.6960 (mt0) REVERT: N 153 GLU cc_start: 0.7987 (pm20) cc_final: 0.7709 (pp20) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.3698 time to fit residues: 61.6980 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 38 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131247 restraints weight = 31475.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136633 restraints weight = 17455.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140333 restraints weight = 11964.874| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6968 Z= 0.151 Angle : 0.723 9.008 9557 Z= 0.339 Chirality : 0.048 0.282 1105 Planarity : 0.005 0.069 1209 Dihedral : 16.585 114.702 1229 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.64 % Favored : 90.24 % Rotamer: Outliers : 3.07 % Allowed : 20.36 % 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: -0.60 (0.28), residues: 871 helix: -1.92 (0.80), residues: 32 sheet: 1.09 (0.30), residues: 312 loop : -1.31 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.006 0.001 HIS A 589 PHE 0.015 0.002 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 0.00236 ( 6) link_NAG-ASN : angle 2.15458 ( 18) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 2.79870 ( 18) hydrogen bonds : bond 0.03704 ( 216) hydrogen bonds : angle 6.16068 ( 582) link_BETA1-6 : bond 0.02505 ( 1) link_BETA1-6 : angle 4.05319 ( 3) SS BOND : bond 0.00435 ( 14) SS BOND : angle 1.25502 ( 28) link_BETA1-3 : bond 0.00775 ( 1) link_BETA1-3 : angle 3.99372 ( 3) covalent geometry : bond 0.00358 ( 6940) covalent geometry : angle 0.69879 ( 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 135 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 2.029 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7166 (ttp80) REVERT: A 487 TRP cc_start: 0.8094 (p-90) cc_final: 0.7681 (p-90) REVERT: E 81 MET cc_start: 0.8808 (ttp) cc_final: 0.8599 (ttp) REVERT: F 82 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: F 91 ASP cc_start: 0.7790 (t0) cc_final: 0.7527 (t0) REVERT: N 153 GLU cc_start: 0.8012 (pm20) cc_final: 0.7774 (pp20) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.4282 time to fit residues: 75.9992 Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 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 F residue 128 THR 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: 0.0470 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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** A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129111 restraints weight = 32317.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134612 restraints weight = 17399.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138312 restraints weight = 11754.732| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2177 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= 0.138 Angle : 0.710 9.621 9557 Z= 0.331 Chirality : 0.047 0.307 1105 Planarity : 0.005 0.063 1209 Dihedral : 15.306 114.489 1229 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.38 % Favored : 91.50 % Rotamer: Outliers : 2.65 % Allowed : 20.08 % Favored : 77.27 % 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: -0.55 (0.29), residues: 871 helix: -1.89 (0.81), residues: 32 sheet: 1.09 (0.30), residues: 309 loop : -1.24 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS A 617 PHE 0.014 0.001 PHE A 509 TYR 0.027 0.001 TYR E 105 ARG 0.003 0.000 ARG M 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 2.13805 ( 18) link_BETA1-4 : bond 0.00555 ( 6) link_BETA1-4 : angle 2.61443 ( 18) hydrogen bonds : bond 0.03458 ( 216) hydrogen bonds : angle 5.95171 ( 582) link_BETA1-6 : bond 0.02487 ( 1) link_BETA1-6 : angle 3.75198 ( 3) SS BOND : bond 0.00373 ( 14) SS BOND : angle 1.16192 ( 28) link_BETA1-3 : bond 0.00631 ( 1) link_BETA1-3 : angle 3.70475 ( 3) covalent geometry : bond 0.00329 ( 6940) covalent geometry : angle 0.68767 ( 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 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.323 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7180 (ttp80) REVERT: A 487 TRP cc_start: 0.8110 (p-90) cc_final: 0.7611 (p-90) REVERT: E 202 ASN cc_start: 0.7871 (t0) cc_final: 0.7641 (t0) REVERT: F 82 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: F 91 ASP cc_start: 0.7746 (t0) cc_final: 0.7481 (t0) REVERT: F 146 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7085 (mt0) REVERT: N 153 GLU cc_start: 0.8079 (pm20) cc_final: 0.7824 (pp20) outliers start: 19 outliers final: 17 residues processed: 124 average time/residue: 0.4169 time to fit residues: 70.3842 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126782 restraints weight = 32500.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132258 restraints weight = 17590.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135929 restraints weight = 11931.151| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6968 Z= 0.174 Angle : 0.726 10.709 9557 Z= 0.342 Chirality : 0.047 0.228 1105 Planarity : 0.005 0.064 1209 Dihedral : 14.447 116.034 1229 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.10 % Favored : 89.78 % Rotamer: Outliers : 2.65 % Allowed : 21.20 % Favored : 76.15 % 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: -2.32 (0.82), residues: 32 sheet: 1.06 (0.30), residues: 309 loop : -1.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 487 HIS 0.007 0.001 HIS A 617 PHE 0.011 0.002 PHE A 550 TYR 0.015 0.002 TYR E 105 ARG 0.003 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 2.52896 ( 18) link_BETA1-4 : bond 0.00555 ( 6) link_BETA1-4 : angle 2.55439 ( 18) hydrogen bonds : bond 0.03517 ( 216) hydrogen bonds : angle 5.90343 ( 582) link_BETA1-6 : bond 0.02322 ( 1) link_BETA1-6 : angle 3.61925 ( 3) SS BOND : bond 0.00425 ( 14) SS BOND : angle 1.28003 ( 28) link_BETA1-3 : bond 0.00920 ( 1) link_BETA1-3 : angle 3.31021 ( 3) covalent geometry : bond 0.00418 ( 6940) covalent geometry : angle 0.70320 ( 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 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.098 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 TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 487 TRP cc_start: 0.8046 (p-90) cc_final: 0.7507 (p-90) REVERT: A 562 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6862 (mmtp) REVERT: E 202 ASN cc_start: 0.7817 (t0) cc_final: 0.7577 (t0) REVERT: F 82 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: F 91 ASP cc_start: 0.7827 (t0) cc_final: 0.7489 (t0) REVERT: F 146 GLN cc_start: 0.7888 (tp-100) cc_final: 0.6972 (mt0) outliers start: 19 outliers final: 17 residues processed: 122 average time/residue: 0.3602 time to fit residues: 60.5388 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE 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: 0.0170 chunk 61 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.161850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128754 restraints weight = 32040.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134292 restraints weight = 17264.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137973 restraints weight = 11680.765| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6968 Z= 0.124 Angle : 0.692 9.263 9557 Z= 0.327 Chirality : 0.046 0.196 1105 Planarity : 0.005 0.063 1209 Dihedral : 13.276 114.569 1229 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 2.51 % Allowed : 21.34 % Favored : 76.15 % 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: -0.50 (0.29), residues: 871 helix: -2.16 (0.83), residues: 32 sheet: 1.15 (0.30), residues: 309 loop : -1.21 (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 0.040 0.002 PHE A 465 TYR 0.018 0.001 TYR E 105 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 6) link_NAG-ASN : angle 2.92382 ( 18) link_BETA1-4 : bond 0.00580 ( 6) link_BETA1-4 : angle 2.41860 ( 18) hydrogen bonds : bond 0.03118 ( 216) hydrogen bonds : angle 5.72402 ( 582) link_BETA1-6 : bond 0.02309 ( 1) link_BETA1-6 : angle 3.57482 ( 3) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.14516 ( 28) link_BETA1-3 : bond 0.00562 ( 1) link_BETA1-3 : angle 3.15057 ( 3) covalent geometry : bond 0.00301 ( 6940) covalent geometry : angle 0.66669 ( 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 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: A 487 TRP cc_start: 0.7994 (p-90) cc_final: 0.7536 (p-90) REVERT: A 557 SER cc_start: 0.7934 (p) cc_final: 0.7706 (m) REVERT: E 202 ASN cc_start: 0.7814 (t0) cc_final: 0.7593 (t0) REVERT: F 82 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: F 91 ASP cc_start: 0.7829 (t0) cc_final: 0.7534 (t0) REVERT: F 146 GLN cc_start: 0.7764 (tp-100) cc_final: 0.6990 (mt0) outliers start: 18 outliers final: 13 residues processed: 118 average time/residue: 0.3601 time to fit residues: 58.1497 Evaluate side-chains 121 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 46 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127212 restraints weight = 32195.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132727 restraints weight = 17425.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136352 restraints weight = 11820.048| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2753 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= 0.157 Angle : 0.694 9.114 9557 Z= 0.331 Chirality : 0.046 0.202 1105 Planarity : 0.005 0.062 1209 Dihedral : 12.825 115.005 1229 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.53 % Favored : 90.36 % Rotamer: Outliers : 2.93 % Allowed : 21.06 % 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: -0.57 (0.29), residues: 871 helix: -2.24 (0.83), residues: 32 sheet: 1.10 (0.30), residues: 309 loop : -1.25 (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 0.031 0.002 PHE A 465 TYR 0.012 0.001 TYR E 106 ARG 0.002 0.000 ARG A 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 6) link_NAG-ASN : angle 3.08856 ( 18) link_BETA1-4 : bond 0.00513 ( 6) link_BETA1-4 : angle 2.32827 ( 18) hydrogen bonds : bond 0.03288 ( 216) hydrogen bonds : angle 5.72092 ( 582) link_BETA1-6 : bond 0.02195 ( 1) link_BETA1-6 : angle 3.65954 ( 3) SS BOND : bond 0.00401 ( 14) SS BOND : angle 1.25222 ( 28) link_BETA1-3 : bond 0.00755 ( 1) link_BETA1-3 : angle 2.62081 ( 3) covalent geometry : bond 0.00375 ( 6940) covalent geometry : angle 0.66773 ( 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 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7353 (ttp80) REVERT: A 487 TRP cc_start: 0.8065 (p-90) cc_final: 0.7503 (p-90) REVERT: A 557 SER cc_start: 0.8031 (p) cc_final: 0.7792 (m) REVERT: A 562 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6806 (mmtp) REVERT: E 89 GLU cc_start: 0.8632 (mp0) cc_final: 0.8046 (mp0) REVERT: E 202 ASN cc_start: 0.7789 (t0) cc_final: 0.7550 (t0) REVERT: F 82 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: F 91 ASP cc_start: 0.7860 (t0) cc_final: 0.7514 (t0) REVERT: F 146 GLN cc_start: 0.7797 (tp-100) cc_final: 0.6933 (mt0) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.3784 time to fit residues: 63.5308 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.160736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127369 restraints weight = 32414.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132918 restraints weight = 17559.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136613 restraints weight = 11886.443| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2907 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= 0.142 Angle : 0.685 8.358 9557 Z= 0.328 Chirality : 0.046 0.212 1105 Planarity : 0.005 0.063 1209 Dihedral : 12.523 114.467 1229 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 2.65 % Allowed : 21.62 % Favored : 75.73 % 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: -0.54 (0.29), residues: 871 helix: -1.43 (0.96), residues: 26 sheet: 1.04 (0.30), residues: 311 loop : -1.25 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.003 0.001 HIS A 617 PHE 0.023 0.002 PHE A 465 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 0.00169 ( 6) link_NAG-ASN : angle 2.98433 ( 18) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 2.25887 ( 18) hydrogen bonds : bond 0.03145 ( 216) hydrogen bonds : angle 5.64395 ( 582) link_BETA1-6 : bond 0.02085 ( 1) link_BETA1-6 : angle 3.61152 ( 3) SS BOND : bond 0.00376 ( 14) SS BOND : angle 1.20538 ( 28) link_BETA1-3 : bond 0.00655 ( 1) link_BETA1-3 : angle 2.28032 ( 3) covalent geometry : bond 0.00341 ( 6940) covalent geometry : angle 0.66055 ( 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 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7356 (ttp80) REVERT: A 487 TRP cc_start: 0.8035 (p-90) cc_final: 0.7523 (p-90) REVERT: A 557 SER cc_start: 0.8023 (p) cc_final: 0.7797 (m) REVERT: A 562 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6832 (mmtp) REVERT: E 89 GLU cc_start: 0.8602 (mp0) cc_final: 0.8034 (mp0) REVERT: E 202 ASN cc_start: 0.7779 (t0) cc_final: 0.7551 (t0) REVERT: F 82 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: F 91 ASP cc_start: 0.7851 (t0) cc_final: 0.7519 (t0) REVERT: F 146 GLN cc_start: 0.7813 (tp-100) cc_final: 0.6992 (mt0) outliers start: 19 outliers final: 16 residues processed: 122 average time/residue: 0.4322 time to fit residues: 70.5978 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 F residue 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 75 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 67 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 overall best weight: 0.2438 ------------------------------------------------------------------------------- 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** M 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130031 restraints weight = 31938.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135700 restraints weight = 16757.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139486 restraints weight = 11156.198| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6968 Z= 0.111 Angle : 0.666 8.068 9557 Z= 0.319 Chirality : 0.045 0.223 1105 Planarity : 0.005 0.061 1209 Dihedral : 12.024 112.430 1229 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 2.23 % Allowed : 22.18 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 871 helix: -0.89 (1.13), residues: 20 sheet: 1.16 (0.30), residues: 311 loop : -1.14 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 469 HIS 0.002 0.001 HIS N 205 PHE 0.024 0.001 PHE A 465 TYR 0.016 0.001 TYR A 611 ARG 0.009 0.000 ARG A 639 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 6) link_NAG-ASN : angle 2.83511 ( 18) link_BETA1-4 : bond 0.00569 ( 6) link_BETA1-4 : angle 2.15990 ( 18) hydrogen bonds : bond 0.02846 ( 216) hydrogen bonds : angle 5.47770 ( 582) link_BETA1-6 : bond 0.01981 ( 1) link_BETA1-6 : angle 3.70288 ( 3) SS BOND : bond 0.00344 ( 14) SS BOND : angle 1.06940 ( 28) link_BETA1-3 : bond 0.00561 ( 1) link_BETA1-3 : angle 1.75520 ( 3) covalent geometry : bond 0.00269 ( 6940) covalent geometry : angle 0.64312 ( 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 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7230 (ttp80) REVERT: A 487 TRP cc_start: 0.8067 (p-90) cc_final: 0.7561 (p-90) REVERT: A 557 SER cc_start: 0.7996 (p) cc_final: 0.7792 (m) REVERT: E 65 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6497 (mm-40) REVERT: E 89 GLU cc_start: 0.8603 (mp0) cc_final: 0.8042 (mp0) REVERT: F 82 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: F 91 ASP cc_start: 0.7746 (t0) cc_final: 0.7487 (t0) REVERT: F 146 GLN cc_start: 0.7750 (tp-100) cc_final: 0.6958 (mt0) outliers start: 16 outliers final: 13 residues processed: 127 average time/residue: 0.4494 time to fit residues: 75.8732 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129469 restraints weight = 32240.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135057 restraints weight = 17171.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138821 restraints weight = 11544.353| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6968 Z= 0.116 Angle : 0.672 8.282 9557 Z= 0.320 Chirality : 0.045 0.225 1105 Planarity : 0.005 0.107 1209 Dihedral : 11.877 112.178 1229 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 2.37 % Allowed : 22.87 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 871 helix: -1.00 (1.09), residues: 21 sheet: 1.18 (0.30), residues: 311 loop : -1.11 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS A 617 PHE 0.023 0.001 PHE A 465 TYR 0.030 0.001 TYR E 150 ARG 0.013 0.000 ARG F 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 2.80317 ( 18) link_BETA1-4 : bond 0.00512 ( 6) link_BETA1-4 : angle 2.13695 ( 18) hydrogen bonds : bond 0.02898 ( 216) hydrogen bonds : angle 5.40433 ( 582) link_BETA1-6 : bond 0.01602 ( 1) link_BETA1-6 : angle 3.74426 ( 3) SS BOND : bond 0.00327 ( 14) SS BOND : angle 1.10114 ( 28) link_BETA1-3 : bond 0.00680 ( 1) link_BETA1-3 : angle 1.59186 ( 3) covalent geometry : bond 0.00286 ( 6940) covalent geometry : angle 0.65017 ( 9487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5323.74 seconds wall clock time: 94 minutes 16.97 seconds (5656.97 seconds total)