Starting phenix.real_space_refine on Sun Nov 17 06:25:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_42041_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_42041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_42041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_42041_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u9y_42041/11_2024/8u9y_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-5513/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: 6.54, per 1000 atoms: 0.50 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: 3.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 19 sheets defined 10.9% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 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: 5.81 Time building geometry restraints manager: 4.16 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: 1.750 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.150 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- 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 6940 Z= 0.341 Angle : 0.821 10.095 9487 Z= 0.383 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 *********************** 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 : 1.057 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: 0.3564 time to fit residues: 54.5074 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 : 1.030 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 6940 Z= 0.255 Angle : 0.769 10.016 9487 Z= 0.366 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 *********************** 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 : 1.026 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: 0.7900 (OUTLIER) cc_final: 0.7049 (ttp80) REVERT: A 626 ILE cc_start: 0.9320 (mm) cc_final: 0.9078 (mt) REVERT: E 81 MET cc_start: 0.8556 (ttp) cc_final: 0.8284 (ttp) REVERT: F 146 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7073 (mt0) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.4252 time to fit residues: 70.9084 Evaluate side-chains 118 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 N residue 206 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6940 Z= 0.279 Angle : 0.732 9.372 9487 Z= 0.351 Chirality : 0.049 0.256 1105 Planarity : 0.005 0.056 1209 Dihedral : 18.722 112.900 1233 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.76 % Favored : 90.13 % Rotamer: Outliers : 2.09 % Allowed : 20.36 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.28), residues: 871 helix: -2.15 (0.77), residues: 32 sheet: 1.03 (0.29), residues: 316 loop : -1.49 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 487 HIS 0.012 0.001 HIS A 589 PHE 0.014 0.002 PHE A 465 TYR 0.012 0.001 TYR E 106 ARG 0.002 0.000 ARG E 56 *********************** 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: 15 poor density : 115 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7259 (ttp80) REVERT: F 146 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7155 (mt0) REVERT: N 206 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7112 (tmmt) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.3670 time to fit residues: 62.1916 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 583 THR Chi-restraints excluded: chain A residue 604 THR 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 M residue 175 SER Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6940 Z= 0.274 Angle : 0.714 9.399 9487 Z= 0.343 Chirality : 0.048 0.272 1105 Planarity : 0.005 0.075 1209 Dihedral : 17.165 114.982 1233 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.76 % Favored : 90.13 % Rotamer: Outliers : 2.79 % Allowed : 20.92 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.28), residues: 871 helix: -2.63 (0.71), residues: 38 sheet: 0.97 (0.30), residues: 311 loop : -1.43 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.008 0.001 HIS A 589 PHE 0.014 0.002 PHE A 465 TYR 0.021 0.001 TYR E 105 ARG 0.002 0.000 ARG M 210 *********************** 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 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7384 (ttp80) REVERT: F 146 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7303 (mt0) REVERT: M 141 ARG cc_start: 0.8878 (tpt90) cc_final: 0.8662 (tpt170) REVERT: N 206 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7400 (tmmt) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.3582 time to fit residues: 62.8621 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 87 CYS Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6940 Z= 0.209 Angle : 0.688 9.229 9487 Z= 0.327 Chirality : 0.048 0.316 1105 Planarity : 0.005 0.070 1209 Dihedral : 15.695 115.006 1233 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.27 % Rotamer: Outliers : 2.37 % Allowed : 20.22 % Favored : 77.41 % 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: -0.68 (0.29), residues: 871 helix: -2.28 (0.81), residues: 32 sheet: 1.05 (0.30), residues: 309 loop : -1.34 (0.26), 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 0.013 0.001 PHE A 509 TYR 0.016 0.001 TYR E 105 ARG 0.001 0.000 ARG M 210 *********************** 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: 17 poor density : 113 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7359 (ttp80) REVERT: A 487 TRP cc_start: 0.7939 (p-90) cc_final: 0.7695 (p-90) REVERT: E 202 ASN cc_start: 0.7933 (t0) cc_final: 0.7724 (t0) REVERT: F 146 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7259 (mt0) REVERT: M 141 ARG cc_start: 0.8861 (tpt90) cc_final: 0.8653 (tpt170) outliers start: 17 outliers final: 15 residues processed: 124 average time/residue: 0.3819 time to fit residues: 63.6675 Evaluate side-chains 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6940 Z= 0.266 Angle : 0.701 10.447 9487 Z= 0.335 Chirality : 0.047 0.267 1105 Planarity : 0.005 0.068 1209 Dihedral : 14.806 116.226 1233 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.22 % Favored : 89.67 % Rotamer: Outliers : 3.07 % Allowed : 20.64 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.73 (0.29), residues: 871 helix: -2.29 (0.83), residues: 32 sheet: 0.99 (0.30), residues: 309 loop : -1.37 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 487 HIS 0.006 0.001 HIS A 617 PHE 0.011 0.001 PHE A 550 TYR 0.013 0.001 TYR E 106 ARG 0.003 0.000 ARG A 455 *********************** 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 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7508 (ttp80) REVERT: A 487 TRP cc_start: 0.7844 (p-90) cc_final: 0.7616 (p-90) REVERT: A 562 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7226 (mmtp) REVERT: F 146 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7189 (mt0) outliers start: 22 outliers final: 20 residues processed: 125 average time/residue: 0.3849 time to fit residues: 64.8726 Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 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 206 LYS 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 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6940 Z= 0.200 Angle : 0.660 9.705 9487 Z= 0.317 Chirality : 0.046 0.196 1105 Planarity : 0.005 0.067 1209 Dihedral : 13.447 115.077 1233 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 3.21 % Allowed : 20.78 % 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: -0.58 (0.29), residues: 871 helix: -1.40 (0.95), residues: 26 sheet: 1.04 (0.30), residues: 311 loop : -1.30 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.001 HIS A 421 PHE 0.011 0.001 PHE A 509 TYR 0.012 0.001 TYR E 105 ARG 0.001 0.000 ARG A 639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7480 (ttp80) REVERT: A 487 TRP cc_start: 0.7837 (p-90) cc_final: 0.7588 (p-90) REVERT: A 562 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7022 (mmtp) REVERT: F 146 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7194 (mt0) REVERT: M 141 ARG cc_start: 0.8834 (tpt90) cc_final: 0.8621 (tpt170) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.3952 time to fit residues: 67.7744 Evaluate side-chains 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 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 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 206 LYS 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 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6940 Z= 0.201 Angle : 0.647 8.338 9487 Z= 0.314 Chirality : 0.045 0.203 1105 Planarity : 0.005 0.065 1209 Dihedral : 12.769 114.418 1233 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.96 % Favored : 90.93 % Rotamer: Outliers : 3.07 % Allowed : 20.78 % 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: -0.54 (0.29), residues: 871 helix: -1.35 (0.94), residues: 26 sheet: 1.06 (0.30), residues: 311 loop : -1.26 (0.27), residues: 534 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 0.046 0.002 PHE A 465 TYR 0.012 0.001 TYR A 611 ARG 0.002 0.000 ARG A 630 *********************** 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 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.069 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: 0.8350 (OUTLIER) cc_final: 0.7504 (ttp80) REVERT: A 487 TRP cc_start: 0.7820 (p-90) cc_final: 0.7565 (p-90) REVERT: A 562 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7118 (mmtp) REVERT: E 65 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6630 (mm-40) REVERT: E 89 GLU cc_start: 0.8338 (mp0) cc_final: 0.8039 (mp0) REVERT: F 146 GLN cc_start: 0.7721 (tp-100) cc_final: 0.7181 (mt0) REVERT: M 141 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8599 (tpt170) outliers start: 22 outliers final: 18 residues processed: 123 average time/residue: 0.3732 time to fit residues: 62.3316 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 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 87 CYS Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 206 LYS 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 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6940 Z= 0.201 Angle : 0.646 8.125 9487 Z= 0.314 Chirality : 0.045 0.212 1105 Planarity : 0.005 0.065 1209 Dihedral : 12.472 113.949 1233 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.73 % 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: -0.52 (0.29), residues: 871 helix: -1.45 (0.91), residues: 27 sheet: 1.08 (0.30), residues: 311 loop : -1.24 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.001 HIS A 617 PHE 0.011 0.001 PHE A 509 TYR 0.012 0.001 TYR A 611 ARG 0.001 0.000 ARG A 630 *********************** 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 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.131 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 revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. REVERT: A 424 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7463 (ttp80) REVERT: A 487 TRP cc_start: 0.7867 (p-90) cc_final: 0.7628 (p-90) REVERT: A 562 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7107 (mmtp) REVERT: E 65 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6691 (mm-40) REVERT: E 89 GLU cc_start: 0.8345 (mp0) cc_final: 0.8044 (mp0) REVERT: F 146 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7176 (mt0) REVERT: M 141 ARG cc_start: 0.8792 (tpt90) cc_final: 0.8591 (tpt170) outliers start: 18 outliers final: 16 residues processed: 122 average time/residue: 0.4231 time to fit residues: 68.6637 Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6940 Z= 0.202 Angle : 0.648 8.111 9487 Z= 0.316 Chirality : 0.045 0.218 1105 Planarity : 0.005 0.097 1209 Dihedral : 12.158 113.257 1229 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.30 % Favored : 90.59 % Rotamer: Outliers : 2.51 % Allowed : 21.48 % 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: -0.50 (0.29), residues: 871 helix: -1.43 (0.91), residues: 27 sheet: 1.09 (0.30), residues: 311 loop : -1.23 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 469 HIS 0.002 0.001 HIS A 617 PHE 0.012 0.001 PHE A 509 TYR 0.012 0.001 TYR A 611 ARG 0.008 0.000 ARG F 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 170 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS M 213 " (corrupted residue). Skipping it. Residue SER 161 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.051 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: 0.8309 (OUTLIER) cc_final: 0.7417 (ttp80) REVERT: A 487 TRP cc_start: 0.7915 (p-90) cc_final: 0.7616 (p-90) REVERT: A 562 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7091 (mmtp) REVERT: E 89 GLU cc_start: 0.8350 (mp0) cc_final: 0.8054 (mp0) REVERT: F 146 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7176 (mt0) outliers start: 18 outliers final: 16 residues processed: 123 average time/residue: 0.4003 time to fit residues: 65.6874 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.161669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128687 restraints weight = 32041.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134304 restraints weight = 17002.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137990 restraints weight = 11431.950| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6940 Z= 0.192 Angle : 0.640 8.293 9487 Z= 0.312 Chirality : 0.045 0.224 1105 Planarity : 0.005 0.069 1209 Dihedral : 11.905 112.298 1229 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.08 % Rotamer: Outliers : 2.79 % Allowed : 21.62 % 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: -0.42 (0.29), residues: 871 helix: -1.02 (1.10), residues: 20 sheet: 1.14 (0.30), residues: 311 loop : -1.19 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS N 205 PHE 0.011 0.001 PHE A 509 TYR 0.013 0.001 TYR A 611 ARG 0.007 0.000 ARG F 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.43 seconds wall clock time: 61 minutes 38.72 seconds (3698.72 seconds total)