Starting phenix.real_space_refine on Mon Jul 28 21:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2025/7mqo_23949.cif" } resolution = 3.4 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= 0.171 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: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 6744 2.51 5 N 1800 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10642 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "E" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" 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: "H" 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: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.76, per 1000 atoms: 0.64 Number of scatterers: 10642 At special positions: 0 Unit cell: (116.025, 137.865, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2004 8.00 N 1800 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=1.92 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.99 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.14 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.07 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E1001 " - " ASN E 215 " " NAG E1002 " - " ASN E 418 " " NAG E1003 " - " ASN E 255 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 397 " " NAG E1006 " - " ASN E 25 " " NAG F1001 " - " ASN F 215 " " NAG F1002 " - " ASN F 418 " " NAG F1003 " - " ASN F 255 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 397 " " NAG F1006 " - " ASN F 25 " " NAG G 1 " - " ASN F 111 " " NAG H 1 " - " ASN E 111 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 15.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.118A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN F 268 " --> pdb=" O HIS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.650A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 693 through 714 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.651A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 693 through 714 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 12 removed outlier: 4.117A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing sheet with id=AA1, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.440A pdb=" N LEU F 33 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'F' and resid 311 through 313 removed outlier: 3.623A pdb=" N ASN F 337 " --> pdb=" O CYS F 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE F 400 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG F 488 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE F 478 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU F 486 " --> pdb=" O ILE F 478 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET F 553 " --> pdb=" O ILE F 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.610A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 567 " --> pdb=" O MET F 504 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 563 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.439A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 232 through 233 Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AB5, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 313 removed outlier: 3.624A pdb=" N ASN E 337 " --> pdb=" O CYS E 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE E 400 " --> pdb=" O PHE E 427 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG E 488 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE E 478 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 486 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE E 485 " --> pdb=" O MET E 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.611A pdb=" N THR E 530 " --> pdb=" O TYR E 507 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 507 " --> pdb=" O THR E 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 567 " --> pdb=" O MET E 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 563 " --> pdb=" O LYS E 508 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3420 1.34 - 1.46: 2464 1.46 - 1.58: 4886 1.58 - 1.70: 2 1.70 - 1.82: 112 Bond restraints: 10884 Sorted by residual: bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" CG PRO E 222 " pdb=" CD PRO E 222 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.07e+00 bond pdb=" CG PRO F 222 " pdb=" CD PRO F 222 " ideal model delta sigma weight residual 1.503 1.427 0.076 3.40e-02 8.65e+02 4.97e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 10879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 13932 1.45 - 2.90: 657 2.90 - 4.35: 117 4.35 - 5.80: 34 5.80 - 7.25: 2 Bond angle restraints: 14742 Sorted by residual: angle pdb=" N PRO E 222 " pdb=" CD PRO E 222 " pdb=" CG PRO E 222 " ideal model delta sigma weight residual 103.20 95.95 7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" N PRO F 222 " pdb=" CD PRO F 222 " pdb=" CG PRO F 222 " ideal model delta sigma weight residual 103.20 95.98 7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 113.01 107.88 5.13 1.20e+00 6.94e-01 1.83e+01 angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 113.01 107.89 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" N ALA D 14 " pdb=" CA ALA D 14 " pdb=" C ALA D 14 " ideal model delta sigma weight residual 113.55 108.74 4.81 1.26e+00 6.30e-01 1.46e+01 ... (remaining 14737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6041 17.69 - 35.39: 604 35.39 - 53.08: 155 53.08 - 70.77: 26 70.77 - 88.47: 10 Dihedral angle restraints: 6836 sinusoidal: 3070 harmonic: 3766 Sorted by residual: dihedral pdb=" CB CYS F 259 " pdb=" SG CYS F 259 " pdb=" SG CYS F 284 " pdb=" CB CYS F 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.96 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS E 259 " pdb=" SG CYS E 259 " pdb=" SG CYS E 284 " pdb=" CB CYS E 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.90 66.90 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS F 8 " pdb=" SG CYS F 8 " pdb=" SG CYS F 26 " pdb=" CB CYS F 26 " ideal model delta sinusoidal sigma weight residual 93.00 156.57 -63.57 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 6833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1301 0.056 - 0.111: 299 0.111 - 0.167: 56 0.167 - 0.222: 4 0.222 - 0.278: 2 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C1 NAG E1002 " pdb=" ND2 ASN E 418 " pdb=" C2 NAG E1002 " pdb=" O5 NAG E1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG F1002 " pdb=" ND2 ASN F 418 " pdb=" C2 NAG F1002 " pdb=" O5 NAG F1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1659 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 8 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO F 9 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 9 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 9 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 8 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO E 9 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 9 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 9 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 221 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO E 222 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " -0.035 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 100 2.60 - 3.18: 9047 3.18 - 3.75: 14987 3.75 - 4.33: 21678 4.33 - 4.90: 35591 Nonbonded interactions: 81403 Sorted by model distance: nonbonded pdb=" OE2 GLU F 443 " pdb=" NE2 GLN F 452 " model vdw 2.030 3.120 nonbonded pdb=" OE2 GLU E 443 " pdb=" NE2 GLN E 452 " model vdw 2.031 3.120 nonbonded pdb=" OD1 ASP F 12 " pdb=" NE2 GLN F 34 " model vdw 2.158 3.120 nonbonded pdb=" OD1 ASP E 12 " pdb=" NE2 GLN E 34 " model vdw 2.159 3.120 nonbonded pdb=" O ILE E 29 " pdb=" OG1 THR E 58 " model vdw 2.268 3.040 ... (remaining 81398 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.000 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.106 10938 Z= 0.203 Angle : 0.768 11.492 14866 Z= 0.403 Chirality : 0.049 0.278 1662 Planarity : 0.005 0.064 1874 Dihedral : 14.608 88.468 4286 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.10 % Favored : 86.75 % Rotamer: Outliers : 0.17 % Allowed : 0.76 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.87 (0.22), residues: 1260 helix: 0.25 (0.39), residues: 188 sheet: -2.53 (0.49), residues: 106 loop : -2.50 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 251 HIS 0.007 0.001 HIS F 21 PHE 0.017 0.002 PHE E 427 TYR 0.019 0.001 TYR E 430 ARG 0.005 0.000 ARG E 488 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 14) link_NAG-ASN : angle 3.58674 ( 42) link_BETA1-4 : bond 0.00021 ( 2) link_BETA1-4 : angle 4.90747 ( 6) hydrogen bonds : bond 0.21951 ( 177) hydrogen bonds : angle 8.41841 ( 483) SS BOND : bond 0.02616 ( 38) SS BOND : angle 2.73399 ( 76) covalent geometry : bond 0.00430 (10884) covalent geometry : angle 0.71348 (14742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 372 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6729 (mtp85) REVERT: E 372 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6595 (mtp85) REVERT: C 10 ILE cc_start: 0.8519 (mt) cc_final: 0.8309 (mt) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.2837 time to fit residues: 60.0968 Evaluate side-chains 122 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 60 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.218593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199605 restraints weight = 11194.775| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.05 r_work: 0.3649 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10938 Z= 0.141 Angle : 0.647 6.472 14866 Z= 0.331 Chirality : 0.046 0.216 1662 Planarity : 0.005 0.045 1874 Dihedral : 6.608 50.473 1739 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.43 % Favored : 88.41 % Rotamer: Outliers : 0.76 % Allowed : 8.70 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.77 (0.23), residues: 1260 helix: 0.58 (0.40), residues: 178 sheet: -2.19 (0.52), residues: 108 loop : -2.49 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 251 HIS 0.004 0.001 HIS F 209 PHE 0.018 0.002 PHE E 565 TYR 0.013 0.001 TYR F 512 ARG 0.009 0.001 ARG F 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 14) link_NAG-ASN : angle 2.06965 ( 42) link_BETA1-4 : bond 0.00256 ( 2) link_BETA1-4 : angle 4.00030 ( 6) hydrogen bonds : bond 0.04740 ( 177) hydrogen bonds : angle 6.66824 ( 483) SS BOND : bond 0.00249 ( 38) SS BOND : angle 1.04973 ( 76) covalent geometry : bond 0.00333 (10884) covalent geometry : angle 0.63027 (14742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8567 (mt) cc_final: 0.8327 (mt) REVERT: F 294 MET cc_start: 0.6573 (ttt) cc_final: 0.6337 (tpt) REVERT: F 372 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7157 (mtp85) REVERT: F 488 ARG cc_start: 0.6694 (mmm-85) cc_final: 0.6450 (mmm-85) REVERT: E 131 ILE cc_start: 0.8582 (mt) cc_final: 0.8321 (mt) REVERT: E 189 GLN cc_start: 0.5544 (tm-30) cc_final: 0.5254 (tm-30) REVERT: E 294 MET cc_start: 0.6624 (ttt) cc_final: 0.6365 (tpt) outliers start: 9 outliers final: 7 residues processed: 155 average time/residue: 0.2192 time to fit residues: 48.5271 Evaluate side-chains 135 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140069 restraints weight = 11390.067| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.82 r_work: 0.3314 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10938 Z= 0.207 Angle : 0.701 6.575 14866 Z= 0.358 Chirality : 0.048 0.162 1662 Planarity : 0.005 0.043 1874 Dihedral : 6.450 49.336 1736 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.54 % Favored : 87.30 % Rotamer: Outliers : 1.86 % Allowed : 11.06 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.89 (0.22), residues: 1260 helix: 0.67 (0.40), residues: 166 sheet: -1.95 (0.51), residues: 106 loop : -2.63 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 251 HIS 0.005 0.001 HIS E 440 PHE 0.019 0.002 PHE F 382 TYR 0.017 0.002 TYR E 60 ARG 0.011 0.001 ARG F 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 14) link_NAG-ASN : angle 1.98137 ( 42) link_BETA1-4 : bond 0.00113 ( 2) link_BETA1-4 : angle 4.03977 ( 6) hydrogen bonds : bond 0.05082 ( 177) hydrogen bonds : angle 6.32073 ( 483) SS BOND : bond 0.00281 ( 38) SS BOND : angle 1.29585 ( 76) covalent geometry : bond 0.00511 (10884) covalent geometry : angle 0.68456 (14742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8472 (mt) cc_final: 0.8217 (mt) REVERT: F 277 TYR cc_start: 0.6190 (m-80) cc_final: 0.5940 (m-80) REVERT: F 294 MET cc_start: 0.6608 (ttt) cc_final: 0.6050 (tpt) REVERT: E 110 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: E 131 ILE cc_start: 0.8501 (mt) cc_final: 0.8274 (mt) REVERT: E 250 ASP cc_start: 0.8258 (t0) cc_final: 0.8051 (t0) REVERT: E 277 TYR cc_start: 0.6147 (m-80) cc_final: 0.5889 (m-80) REVERT: E 294 MET cc_start: 0.6626 (ttt) cc_final: 0.6034 (tpt) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.2052 time to fit residues: 45.6011 Evaluate side-chains 140 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 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 5 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.196769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143411 restraints weight = 11268.139| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.45 r_work: 0.3463 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10938 Z= 0.138 Angle : 0.617 6.243 14866 Z= 0.318 Chirality : 0.045 0.159 1662 Planarity : 0.004 0.043 1874 Dihedral : 6.312 52.065 1736 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.11 % Favored : 88.73 % Rotamer: Outliers : 2.20 % Allowed : 13.09 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.77 (0.22), residues: 1260 helix: 0.91 (0.41), residues: 166 sheet: -1.79 (0.52), residues: 106 loop : -2.58 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 PHE 0.014 0.002 PHE F 705 TYR 0.010 0.001 TYR F 507 ARG 0.009 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 14) link_NAG-ASN : angle 1.80918 ( 42) link_BETA1-4 : bond 0.00036 ( 2) link_BETA1-4 : angle 3.79961 ( 6) hydrogen bonds : bond 0.04125 ( 177) hydrogen bonds : angle 6.13362 ( 483) SS BOND : bond 0.00240 ( 38) SS BOND : angle 0.95117 ( 76) covalent geometry : bond 0.00335 (10884) covalent geometry : angle 0.60377 (14742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: F 131 ILE cc_start: 0.8599 (mt) cc_final: 0.8364 (mt) REVERT: F 256 PHE cc_start: 0.7721 (t80) cc_final: 0.7043 (t80) REVERT: F 260 GLN cc_start: 0.6910 (mt0) cc_final: 0.6605 (mp10) REVERT: E 12 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: E 131 ILE cc_start: 0.8626 (mt) cc_final: 0.8395 (mt) REVERT: E 256 PHE cc_start: 0.7691 (t80) cc_final: 0.7306 (t80) REVERT: E 260 GLN cc_start: 0.6836 (mt0) cc_final: 0.6331 (mt0) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.2144 time to fit residues: 46.3314 Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 0.0270 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.196955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141386 restraints weight = 11314.583| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.49 r_work: 0.3363 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10938 Z= 0.120 Angle : 0.590 5.977 14866 Z= 0.304 Chirality : 0.044 0.150 1662 Planarity : 0.004 0.044 1874 Dihedral : 6.172 52.438 1736 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 1.86 % Allowed : 14.36 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.72 (0.22), residues: 1260 helix: 1.06 (0.41), residues: 166 sheet: -1.76 (0.51), residues: 110 loop : -2.57 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 PHE 0.014 0.001 PHE F 705 TYR 0.010 0.001 TYR F 507 ARG 0.010 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 14) link_NAG-ASN : angle 1.73416 ( 42) link_BETA1-4 : bond 0.00087 ( 2) link_BETA1-4 : angle 3.62208 ( 6) hydrogen bonds : bond 0.03722 ( 177) hydrogen bonds : angle 5.93021 ( 483) SS BOND : bond 0.00253 ( 38) SS BOND : angle 0.74452 ( 76) covalent geometry : bond 0.00286 (10884) covalent geometry : angle 0.57781 (14742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: F 131 ILE cc_start: 0.8429 (mt) cc_final: 0.8181 (mt) REVERT: E 66 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8352 (p) REVERT: E 131 ILE cc_start: 0.8437 (mt) cc_final: 0.8204 (mt) REVERT: E 151 ASP cc_start: 0.7020 (m-30) cc_final: 0.6759 (m-30) REVERT: E 416 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.7008 (pmtt) REVERT: D 13 GLU cc_start: 0.7995 (tp30) cc_final: 0.7750 (mm-30) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.2388 time to fit residues: 47.8411 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.197604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142115 restraints weight = 11386.914| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.49 r_work: 0.3353 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10938 Z= 0.124 Angle : 0.589 7.270 14866 Z= 0.303 Chirality : 0.044 0.149 1662 Planarity : 0.004 0.045 1874 Dihedral : 6.108 52.688 1736 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.75 % Favored : 88.17 % Rotamer: Outliers : 2.20 % Allowed : 14.95 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.69 (0.22), residues: 1260 helix: 1.08 (0.41), residues: 166 sheet: -1.74 (0.51), residues: 110 loop : -2.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 251 HIS 0.005 0.001 HIS D 5 PHE 0.016 0.001 PHE F 256 TYR 0.011 0.001 TYR F 507 ARG 0.012 0.000 ARG F 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 14) link_NAG-ASN : angle 1.72557 ( 42) link_BETA1-4 : bond 0.00040 ( 2) link_BETA1-4 : angle 3.48061 ( 6) hydrogen bonds : bond 0.03701 ( 177) hydrogen bonds : angle 6.00194 ( 483) SS BOND : bond 0.00225 ( 38) SS BOND : angle 0.74513 ( 76) covalent geometry : bond 0.00301 (10884) covalent geometry : angle 0.57792 (14742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: F 131 ILE cc_start: 0.8420 (mt) cc_final: 0.8174 (mt) REVERT: F 256 PHE cc_start: 0.7647 (t80) cc_final: 0.7275 (t80) REVERT: F 260 GLN cc_start: 0.6902 (mt0) cc_final: 0.6123 (mt0) REVERT: E 12 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: E 123 ASN cc_start: 0.8427 (m110) cc_final: 0.8196 (m110) REVERT: E 131 ILE cc_start: 0.8423 (mt) cc_final: 0.8193 (mt) REVERT: E 151 ASP cc_start: 0.6915 (m-30) cc_final: 0.6640 (m-30) outliers start: 26 outliers final: 21 residues processed: 144 average time/residue: 0.2660 time to fit residues: 56.5843 Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.219077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186916 restraints weight = 11430.617| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.09 r_work: 0.3683 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10938 Z= 0.131 Angle : 0.601 6.542 14866 Z= 0.309 Chirality : 0.044 0.175 1662 Planarity : 0.004 0.051 1874 Dihedral : 6.090 53.059 1736 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.14 % Favored : 87.78 % Rotamer: Outliers : 2.45 % Allowed : 15.29 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.67 (0.22), residues: 1260 helix: 1.12 (0.41), residues: 166 sheet: -1.74 (0.51), residues: 110 loop : -2.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 251 HIS 0.003 0.001 HIS E 21 PHE 0.013 0.001 PHE F 705 TYR 0.011 0.001 TYR F 507 ARG 0.013 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 14) link_NAG-ASN : angle 1.73547 ( 42) link_BETA1-4 : bond 0.00071 ( 2) link_BETA1-4 : angle 3.39871 ( 6) hydrogen bonds : bond 0.03716 ( 177) hydrogen bonds : angle 5.90201 ( 483) SS BOND : bond 0.00235 ( 38) SS BOND : angle 1.06609 ( 76) covalent geometry : bond 0.00321 (10884) covalent geometry : angle 0.58756 (14742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: F 131 ILE cc_start: 0.8764 (mt) cc_final: 0.8539 (mt) REVERT: E 12 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: E 131 ILE cc_start: 0.8779 (mt) cc_final: 0.8575 (mt) REVERT: E 151 ASP cc_start: 0.7338 (m-30) cc_final: 0.7105 (m-30) outliers start: 29 outliers final: 22 residues processed: 150 average time/residue: 0.1986 time to fit residues: 44.0196 Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.219556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.193232 restraints weight = 11289.837| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.46 r_work: 0.3733 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10938 Z= 0.125 Angle : 0.600 6.190 14866 Z= 0.310 Chirality : 0.044 0.162 1662 Planarity : 0.004 0.042 1874 Dihedral : 6.075 53.195 1736 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.06 % Favored : 87.86 % Rotamer: Outliers : 2.53 % Allowed : 15.37 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.63 (0.22), residues: 1260 helix: 1.27 (0.41), residues: 166 sheet: -1.69 (0.51), residues: 110 loop : -2.53 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 183 HIS 0.004 0.001 HIS E 263 PHE 0.014 0.001 PHE F 705 TYR 0.011 0.001 TYR F 507 ARG 0.011 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 14) link_NAG-ASN : angle 1.68525 ( 42) link_BETA1-4 : bond 0.00091 ( 2) link_BETA1-4 : angle 3.33257 ( 6) hydrogen bonds : bond 0.03601 ( 177) hydrogen bonds : angle 5.80837 ( 483) SS BOND : bond 0.00214 ( 38) SS BOND : angle 1.12824 ( 76) covalent geometry : bond 0.00305 (10884) covalent geometry : angle 0.58677 (14742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: E 131 ILE cc_start: 0.8798 (mt) cc_final: 0.8542 (mt) outliers start: 30 outliers final: 25 residues processed: 150 average time/residue: 0.2516 time to fit residues: 55.5883 Evaluate side-chains 151 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 0.0980 chunk 100 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN F 108 ASN F 405 ASN F 429 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.216279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.194822 restraints weight = 11309.469| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.22 r_work: 0.3859 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10938 Z= 0.124 Angle : 0.604 7.318 14866 Z= 0.311 Chirality : 0.044 0.156 1662 Planarity : 0.004 0.034 1874 Dihedral : 6.062 53.132 1736 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.98 % Favored : 87.94 % Rotamer: Outliers : 2.79 % Allowed : 15.29 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.59 (0.22), residues: 1260 helix: 1.30 (0.41), residues: 166 sheet: -1.64 (0.52), residues: 110 loop : -2.51 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 183 HIS 0.005 0.001 HIS F 429 PHE 0.017 0.001 PHE F 256 TYR 0.010 0.001 TYR F 507 ARG 0.011 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 14) link_NAG-ASN : angle 1.65647 ( 42) link_BETA1-4 : bond 0.00134 ( 2) link_BETA1-4 : angle 3.28197 ( 6) hydrogen bonds : bond 0.03512 ( 177) hydrogen bonds : angle 5.73273 ( 483) SS BOND : bond 0.00209 ( 38) SS BOND : angle 1.01792 ( 76) covalent geometry : bond 0.00299 (10884) covalent geometry : angle 0.59159 (14742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8479 (mm) cc_final: 0.8251 (mm) REVERT: E 12 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7541 (m-30) outliers start: 33 outliers final: 30 residues processed: 149 average time/residue: 0.2912 time to fit residues: 64.1613 Evaluate side-chains 153 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 429 HIS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 117 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 115 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN F 405 ASN F 429 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 21 HIS C 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.215864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188969 restraints weight = 11263.837| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.45 r_work: 0.3736 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10938 Z= 0.127 Angle : 0.608 5.953 14866 Z= 0.314 Chirality : 0.045 0.145 1662 Planarity : 0.004 0.033 1874 Dihedral : 6.062 53.274 1736 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.90 % Favored : 88.02 % Rotamer: Outliers : 2.70 % Allowed : 15.37 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.59 (0.22), residues: 1260 helix: 1.31 (0.41), residues: 166 sheet: -1.62 (0.52), residues: 110 loop : -2.52 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 183 HIS 0.005 0.001 HIS C 21 PHE 0.014 0.001 PHE F 705 TYR 0.020 0.001 TYR E 127 ARG 0.013 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 14) link_NAG-ASN : angle 1.65005 ( 42) link_BETA1-4 : bond 0.00081 ( 2) link_BETA1-4 : angle 3.24280 ( 6) hydrogen bonds : bond 0.03532 ( 177) hydrogen bonds : angle 5.71474 ( 483) SS BOND : bond 0.00213 ( 38) SS BOND : angle 0.96656 ( 76) covalent geometry : bond 0.00310 (10884) covalent geometry : angle 0.59708 (14742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8470 (mm) cc_final: 0.8233 (mm) REVERT: E 12 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7296 (m-30) outliers start: 32 outliers final: 29 residues processed: 142 average time/residue: 0.2016 time to fit residues: 42.0519 Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 92 optimal weight: 0.0170 chunk 109 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN F 405 ASN F 429 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.216324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.189664 restraints weight = 11172.224| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.52 r_work: 0.3758 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10938 Z= 0.128 Angle : 0.610 6.957 14866 Z= 0.315 Chirality : 0.044 0.145 1662 Planarity : 0.004 0.034 1874 Dihedral : 6.054 53.434 1736 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.46 % Favored : 87.46 % Rotamer: Outliers : 2.70 % Allowed : 15.46 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.59 (0.22), residues: 1260 helix: 1.34 (0.41), residues: 166 sheet: -1.62 (0.52), residues: 110 loop : -2.52 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 183 HIS 0.005 0.001 HIS F 429 PHE 0.018 0.001 PHE F 256 TYR 0.014 0.001 TYR E 127 ARG 0.019 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 14) link_NAG-ASN : angle 1.63377 ( 42) link_BETA1-4 : bond 0.00064 ( 2) link_BETA1-4 : angle 3.21476 ( 6) hydrogen bonds : bond 0.03534 ( 177) hydrogen bonds : angle 5.68866 ( 483) SS BOND : bond 0.00210 ( 38) SS BOND : angle 0.88380 ( 76) covalent geometry : bond 0.00311 (10884) covalent geometry : angle 0.60001 (14742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5711.01 seconds wall clock time: 102 minutes 39.36 seconds (6159.36 seconds total)