Starting phenix.real_space_refine on Sun Dec 29 14:40:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqo_23949/12_2024/7mqo_23949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqo_23949/12_2024/7mqo_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_23949/12_2024/7mqo_23949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqo_23949/12_2024/7mqo_23949.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqo_23949/12_2024/7mqo_23949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqo_23949/12_2024/7mqo_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-5532/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: 7.06, per 1000 atoms: 0.66 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 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: 1.22 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: 3.50 Time building geometry restraints manager: 3.41 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: 0.910 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- 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 : 0.004 0.093 10884 Z= 0.286 Angle : 0.713 7.252 14742 Z= 0.387 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 *********************** 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 : 1.230 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: 0.2413 time to fit residues: 51.3060 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 : 1.221 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 10884 Z= 0.221 Angle : 0.630 5.172 14742 Z= 0.327 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 *********************** 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 : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8532 (mt) cc_final: 0.8304 (mt) REVERT: F 372 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6688 (mtp85) REVERT: F 488 ARG cc_start: 0.6646 (mmm-85) cc_final: 0.6428 (mmm-85) REVERT: E 131 ILE cc_start: 0.8542 (mt) cc_final: 0.8290 (mt) REVERT: E 189 GLN cc_start: 0.5359 (tm-30) cc_final: 0.5115 (tm-30) outliers start: 9 outliers final: 7 residues processed: 155 average time/residue: 0.2329 time to fit residues: 51.8211 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 : 1.157 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 0.0170 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10884 Z= 0.221 Angle : 0.601 6.250 14742 Z= 0.313 Chirality : 0.045 0.163 1662 Planarity : 0.004 0.038 1874 Dihedral : 6.188 47.941 1736 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.59 % Favored : 88.25 % Rotamer: Outliers : 1.60 % Allowed : 10.47 % Favored : 87.92 % 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: -2.83 (0.22), residues: 1260 helix: 0.62 (0.40), residues: 182 sheet: -1.95 (0.49), residues: 118 loop : -2.61 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 251 HIS 0.004 0.001 HIS E 247 PHE 0.018 0.002 PHE E 565 TYR 0.011 0.001 TYR E 512 ARG 0.013 0.001 ARG F 409 *********************** 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 154 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8589 (mt) cc_final: 0.8363 (mt) REVERT: F 260 GLN cc_start: 0.6595 (mt0) cc_final: 0.6265 (mt0) REVERT: E 131 ILE cc_start: 0.8616 (mt) cc_final: 0.8405 (mt) outliers start: 19 outliers final: 16 residues processed: 146 average time/residue: 0.2114 time to fit residues: 44.9953 Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 184 THR 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 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 416 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0970 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 109 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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 ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10884 Z= 0.169 Angle : 0.560 4.574 14742 Z= 0.292 Chirality : 0.044 0.162 1662 Planarity : 0.004 0.043 1874 Dihedral : 6.022 48.621 1736 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.56 % Favored : 89.37 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % Favored : 85.73 % 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: -2.74 (0.23), residues: 1260 helix: 0.80 (0.40), residues: 180 sheet: -1.81 (0.49), residues: 118 loop : -2.57 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 251 HIS 0.004 0.001 HIS E 21 PHE 0.013 0.001 PHE E 565 TYR 0.009 0.001 TYR E 512 ARG 0.010 0.000 ARG E 409 *********************** 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 157 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 66 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8183 (p) REVERT: F 256 PHE cc_start: 0.7732 (t80) cc_final: 0.7415 (t80) REVERT: F 260 GLN cc_start: 0.6664 (mt0) cc_final: 0.6323 (mt0) outliers start: 21 outliers final: 11 residues processed: 151 average time/residue: 0.2124 time to fit residues: 47.1955 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 342 ILE 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 120 GLU Chi-restraints excluded: chain E residue 238 VAL 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 101 optimal weight: 0.0020 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 122 ASN E 122 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10884 Z= 0.333 Angle : 0.685 6.736 14742 Z= 0.355 Chirality : 0.048 0.152 1662 Planarity : 0.005 0.043 1874 Dihedral : 6.368 51.838 1736 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 2.62 % Allowed : 13.60 % 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: -2.84 (0.22), residues: 1260 helix: 0.72 (0.40), residues: 166 sheet: -1.93 (0.50), residues: 110 loop : -2.59 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 133 HIS 0.005 0.001 HIS E 100 PHE 0.019 0.002 PHE E 382 TYR 0.017 0.002 TYR E 60 ARG 0.013 0.001 ARG E 409 *********************** 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 166 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: F 277 TYR cc_start: 0.6793 (m-80) cc_final: 0.6510 (m-80) REVERT: E 277 TYR cc_start: 0.6704 (m-80) cc_final: 0.6402 (m-80) outliers start: 31 outliers final: 25 residues processed: 157 average time/residue: 0.2312 time to fit residues: 53.2708 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 : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU 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 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 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 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 416 LYS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10884 Z= 0.233 Angle : 0.607 5.377 14742 Z= 0.316 Chirality : 0.045 0.149 1662 Planarity : 0.004 0.045 1874 Dihedral : 6.266 51.962 1736 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 1.86 % Allowed : 15.03 % Favored : 83.11 % 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: -2.76 (0.22), residues: 1260 helix: 0.96 (0.41), residues: 166 sheet: -1.91 (0.51), residues: 110 loop : -2.56 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 251 HIS 0.003 0.001 HIS E 21 PHE 0.014 0.002 PHE F 256 TYR 0.011 0.001 TYR F 507 ARG 0.014 0.000 ARG F 409 *********************** 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 153 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: E 12 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7329 (m-30) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 0.2170 time to fit residues: 45.7473 Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 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 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE 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 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10884 Z= 0.208 Angle : 0.610 6.756 14742 Z= 0.317 Chirality : 0.045 0.169 1662 Planarity : 0.004 0.037 1874 Dihedral : 6.198 51.956 1736 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.67 % Favored : 88.25 % Rotamer: Outliers : 2.20 % Allowed : 15.71 % 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: -2.70 (0.22), residues: 1260 helix: 1.10 (0.41), residues: 166 sheet: -1.86 (0.51), residues: 110 loop : -2.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 183 HIS 0.006 0.001 HIS D 5 PHE 0.014 0.001 PHE F 705 TYR 0.011 0.001 TYR F 507 ARG 0.009 0.000 ARG F 409 *********************** 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 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7414 (m-30) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.2229 time to fit residues: 46.8486 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 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 478 ILE 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 266 CYS 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 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 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10884 Z= 0.220 Angle : 0.610 6.654 14742 Z= 0.317 Chirality : 0.045 0.181 1662 Planarity : 0.004 0.060 1874 Dihedral : 6.157 53.047 1736 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.46 % Favored : 87.46 % Rotamer: Outliers : 2.45 % Allowed : 15.46 % 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: -2.68 (0.22), residues: 1260 helix: 1.29 (0.42), residues: 160 sheet: -1.77 (0.52), residues: 110 loop : -2.55 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.003 0.001 HIS D 5 PHE 0.016 0.002 PHE E 256 TYR 0.011 0.001 TYR F 507 ARG 0.015 0.001 ARG F 409 *********************** 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 163 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8401 (mm) cc_final: 0.8148 (mm) REVERT: F 12 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: F 294 MET cc_start: 0.5529 (tpt) cc_final: 0.5310 (ttt) REVERT: E 12 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: E 487 LEU cc_start: 0.6715 (mp) cc_final: 0.6432 (mp) REVERT: D 13 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7439 (mm-30) outliers start: 29 outliers final: 22 residues processed: 152 average time/residue: 0.2231 time to fit residues: 49.3241 Evaluate side-chains 149 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 21 HIS 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 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 478 ILE 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 238 VAL Chi-restraints excluded: chain E residue 266 CYS 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 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 113 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10884 Z= 0.350 Angle : 0.682 6.243 14742 Z= 0.355 Chirality : 0.048 0.168 1662 Planarity : 0.005 0.048 1874 Dihedral : 6.394 54.790 1736 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.41 % Favored : 86.51 % Rotamer: Outliers : 2.45 % Allowed : 15.71 % 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: -2.78 (0.22), residues: 1260 helix: 1.08 (0.41), residues: 160 sheet: -1.74 (0.52), residues: 110 loop : -2.61 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 183 HIS 0.005 0.001 HIS D 5 PHE 0.018 0.002 PHE F 427 TYR 0.015 0.002 TYR E 60 ARG 0.019 0.001 ARG F 409 *********************** 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 160 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8499 (mm) cc_final: 0.8188 (mt) REVERT: F 12 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: E 12 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: E 487 LEU cc_start: 0.6847 (mp) cc_final: 0.6575 (mp) REVERT: D 13 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.2289 time to fit residues: 49.1393 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 182 CYS 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 478 ILE 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 266 CYS 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 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 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** F 209 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10884 Z= 0.229 Angle : 0.634 6.820 14742 Z= 0.330 Chirality : 0.045 0.199 1662 Planarity : 0.004 0.048 1874 Dihedral : 6.274 54.719 1736 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.90 % Favored : 87.94 % Rotamer: Outliers : 2.20 % Allowed : 16.05 % Favored : 81.76 % 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: 1.30 (0.42), residues: 160 sheet: -1.68 (0.53), residues: 110 loop : -2.58 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 183 HIS 0.005 0.001 HIS B 5 PHE 0.017 0.002 PHE E 256 TYR 0.012 0.001 TYR F 507 ARG 0.018 0.001 ARG F 409 ********************** 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 154 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8461 (mm) cc_final: 0.8233 (mt) REVERT: F 12 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: E 12 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: E 294 MET cc_start: 0.5652 (tpt) cc_final: 0.5308 (ttt) REVERT: E 487 LEU cc_start: 0.6763 (mp) cc_final: 0.6514 (mp) outliers start: 26 outliers final: 22 residues processed: 145 average time/residue: 0.2248 time to fit residues: 47.2551 Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 478 ILE 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 266 CYS 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 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 30 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.213152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188252 restraints weight = 11053.005| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.52 r_work: 0.3470 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10884 Z= 0.241 Angle : 0.634 6.485 14742 Z= 0.329 Chirality : 0.045 0.180 1662 Planarity : 0.004 0.051 1874 Dihedral : 6.242 55.558 1736 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.70 % Favored : 87.14 % Rotamer: Outliers : 2.45 % Allowed : 16.05 % Favored : 81.50 % 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: 1.36 (0.42), residues: 160 sheet: -1.63 (0.53), residues: 110 loop : -2.57 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 183 HIS 0.004 0.001 HIS E 429 PHE 0.014 0.002 PHE E 705 TYR 0.011 0.001 TYR F 507 ARG 0.019 0.001 ARG F 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.72 seconds wall clock time: 42 minutes 1.80 seconds (2521.80 seconds total)