Starting phenix.real_space_refine on Sat Aug 3 23:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/08_2024/8tve_41639.cif" } resolution = 3.9 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= 0.016 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 48 5.16 5 C 5799 2.51 5 N 1536 2.21 5 O 1707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9090 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.18, per 1000 atoms: 0.79 Number of scatterers: 9090 At special positions: 0 Unit cell: (84.96, 85.845, 171.69, 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 48 16.00 O 1707 8.00 N 1536 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.06 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.06 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.06 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG A 602 " - " ASN A 459 " " NAG B 601 " - " ASN B 65 " " NAG B 602 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 602 " - " ASN C 459 " Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 18 sheets defined 42.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 92 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 141 through 178 Processing helix chain 'A' and resid 178 through 207 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 92 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 141 through 178 Processing helix chain 'B' and resid 178 through 207 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 476 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 92 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 141 through 178 Processing helix chain 'C' and resid 178 through 207 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'C' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 removed outlier: 5.344A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 310 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 removed outlier: 7.012A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLY B 431 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 51 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR B 433 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 53 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.031A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.526A pdb=" N THR A 394 " --> pdb=" O CYS A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 removed outlier: 6.900A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 38 removed outlier: 5.345A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 removed outlier: 7.012A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLY C 431 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 51 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR C 433 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 53 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374 removed outlier: 4.032A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.525A pdb=" N THR B 394 " --> pdb=" O CYS B 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 38 removed outlier: 5.344A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374 removed outlier: 4.031A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.525A pdb=" N THR C 394 " --> pdb=" O CYS C 389 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1530 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: 3.42 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2310 1.33 - 1.46: 2146 1.46 - 1.59: 4691 1.59 - 1.71: 3 1.71 - 1.84: 66 Bond restraints: 9216 Sorted by residual: bond pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB LEU B 23 " pdb=" CG LEU B 23 " ideal model delta sigma weight residual 1.530 1.601 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB LEU C 23 " pdb=" CG LEU C 23 " ideal model delta sigma weight residual 1.530 1.601 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NE ARG C 171 " pdb=" CZ ARG C 171 " ideal model delta sigma weight residual 1.326 1.362 -0.036 1.10e-02 8.26e+03 1.07e+01 bond pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sigma weight residual 1.326 1.362 -0.036 1.10e-02 8.26e+03 1.05e+01 ... (remaining 9211 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.34: 350 107.34 - 113.90: 5049 113.90 - 120.46: 3864 120.46 - 127.03: 3283 127.03 - 133.59: 27 Bond angle restraints: 12573 Sorted by residual: angle pdb=" N ASN C 464 " pdb=" CA ASN C 464 " pdb=" C ASN C 464 " ideal model delta sigma weight residual 111.36 101.68 9.68 1.09e+00 8.42e-01 7.89e+01 angle pdb=" N ASN B 464 " pdb=" CA ASN B 464 " pdb=" C ASN B 464 " ideal model delta sigma weight residual 111.36 101.68 9.68 1.09e+00 8.42e-01 7.88e+01 angle pdb=" N ASN A 464 " pdb=" CA ASN A 464 " pdb=" C ASN A 464 " ideal model delta sigma weight residual 111.36 101.69 9.67 1.09e+00 8.42e-01 7.88e+01 angle pdb=" N MET C 142 " pdb=" CA MET C 142 " pdb=" C MET C 142 " ideal model delta sigma weight residual 111.28 101.66 9.62 1.09e+00 8.42e-01 7.79e+01 angle pdb=" N MET A 142 " pdb=" CA MET A 142 " pdb=" C MET A 142 " ideal model delta sigma weight residual 111.28 101.67 9.61 1.09e+00 8.42e-01 7.77e+01 ... (remaining 12568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 5451 16.38 - 32.75: 183 32.75 - 49.13: 33 49.13 - 65.50: 21 65.50 - 81.88: 12 Dihedral angle restraints: 5700 sinusoidal: 2118 harmonic: 3582 Sorted by residual: dihedral pdb=" CB CYS B 389 " pdb=" SG CYS B 389 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 412 " pdb=" CB CYS A 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 940 0.070 - 0.139: 466 0.139 - 0.208: 118 0.208 - 0.278: 30 0.278 - 0.347: 9 Chirality restraints: 1563 Sorted by residual: chirality pdb=" C2 NAG B 602 " pdb=" C1 NAG B 602 " pdb=" C3 NAG B 602 " pdb=" N2 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C2 NAG A 602 " pdb=" C1 NAG A 602 " pdb=" C3 NAG A 602 " pdb=" N2 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 NAG C 602 " pdb=" C1 NAG C 602 " pdb=" C3 NAG C 602 " pdb=" N2 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1560 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 65 " 0.028 2.00e-02 2.50e+03 2.98e-02 1.11e+01 pdb=" CG ASN B 65 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 65 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 65 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 65 " 0.028 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN A 65 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 65 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 65 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 65 " -0.027 2.00e-02 2.50e+03 2.97e-02 1.10e+01 pdb=" CG ASN C 65 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 65 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 65 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.036 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3860 2.93 - 3.42: 8456 3.42 - 3.91: 14542 3.91 - 4.41: 15317 4.41 - 4.90: 25936 Nonbonded interactions: 68111 Sorted by model distance: nonbonded pdb=" N THR B 392 " pdb=" N ASP B 393 " model vdw 2.433 2.560 nonbonded pdb=" N THR C 392 " pdb=" N ASP C 393 " model vdw 2.433 2.560 nonbonded pdb=" N THR A 392 " pdb=" N ASP A 393 " model vdw 2.433 2.560 nonbonded pdb=" N SER B 356 " pdb=" O SER B 356 " model vdw 2.513 2.496 nonbonded pdb=" N SER C 356 " pdb=" O SER C 356 " model vdw 2.513 2.496 ... (remaining 68106 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.840 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 30.730 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.013 0.072 9216 Z= 0.828 Angle : 1.522 11.409 12573 Z= 1.074 Chirality : 0.087 0.347 1563 Planarity : 0.005 0.020 1614 Dihedral : 9.806 79.964 3345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1209 helix: 0.53 (0.20), residues: 504 sheet: 0.73 (0.40), residues: 159 loop : -0.14 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP A 303 HIS 0.002 0.001 HIS C 253 PHE 0.016 0.004 PHE B 230 TYR 0.027 0.005 TYR B 202 ARG 0.004 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 0.954 Fit side-chains REVERT: B 217 VAL cc_start: 0.9116 (t) cc_final: 0.8912 (m) REVERT: B 404 VAL cc_start: 0.8501 (t) cc_final: 0.8275 (t) REVERT: B 473 GLU cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0) REVERT: C 463 GLN cc_start: 0.7851 (mm110) cc_final: 0.7644 (mm110) outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.2604 time to fit residues: 54.3030 Evaluate side-chains 85 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 31 optimal weight: 0.0170 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 352 GLN B 95 ASN B 352 GLN C 95 ASN C 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.213 Angle : 0.586 6.324 12573 Z= 0.325 Chirality : 0.045 0.140 1563 Planarity : 0.004 0.029 1614 Dihedral : 4.844 18.970 1431 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.21 % Allowed : 7.09 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1209 helix: 2.65 (0.23), residues: 510 sheet: 0.59 (0.39), residues: 150 loop : -0.30 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 303 HIS 0.001 0.000 HIS C 253 PHE 0.011 0.002 PHE C 209 TYR 0.019 0.002 TYR C 427 ARG 0.003 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.025 Fit side-chains REVERT: B 217 VAL cc_start: 0.9004 (t) cc_final: 0.8743 (m) REVERT: B 447 ASP cc_start: 0.8139 (m-30) cc_final: 0.7898 (m-30) REVERT: C 427 TYR cc_start: 0.8341 (t80) cc_final: 0.8108 (t80) outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 0.2107 time to fit residues: 33.0238 Evaluate side-chains 72 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.0060 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 37 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.200 Angle : 0.522 5.594 12573 Z= 0.287 Chirality : 0.044 0.139 1563 Planarity : 0.003 0.035 1614 Dihedral : 4.257 17.570 1431 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.65 % Allowed : 7.09 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.24), residues: 1209 helix: 3.03 (0.24), residues: 513 sheet: 0.78 (0.40), residues: 150 loop : -0.35 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 303 HIS 0.001 0.001 HIS B 253 PHE 0.008 0.001 PHE B 277 TYR 0.016 0.001 TYR C 427 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 74 time to evaluate : 1.034 Fit side-chains REVERT: B 217 VAL cc_start: 0.9089 (t) cc_final: 0.8755 (m) REVERT: C 427 TYR cc_start: 0.8296 (t80) cc_final: 0.7921 (t80) outliers start: 33 outliers final: 16 residues processed: 104 average time/residue: 0.1977 time to fit residues: 29.9182 Evaluate side-chains 78 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 266 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.0970 chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9216 Z= 0.224 Angle : 0.518 5.662 12573 Z= 0.281 Chirality : 0.044 0.138 1563 Planarity : 0.003 0.038 1614 Dihedral : 4.192 17.325 1431 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.10 % Allowed : 8.86 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1209 helix: 2.95 (0.23), residues: 516 sheet: 0.79 (0.42), residues: 150 loop : -0.38 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 303 HIS 0.002 0.001 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.020 0.002 TYR A 427 ARG 0.001 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 185 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6700 (tt) REVERT: A 467 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6978 (t0) REVERT: C 424 VAL cc_start: 0.8117 (t) cc_final: 0.7899 (p) REVERT: C 427 TYR cc_start: 0.8282 (t80) cc_final: 0.7809 (t80) outliers start: 28 outliers final: 18 residues processed: 94 average time/residue: 0.1778 time to fit residues: 24.9851 Evaluate side-chains 84 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9216 Z= 0.244 Angle : 0.531 6.585 12573 Z= 0.283 Chirality : 0.044 0.181 1563 Planarity : 0.004 0.042 1614 Dihedral : 4.176 17.353 1431 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.54 % Allowed : 9.52 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1209 helix: 2.96 (0.23), residues: 516 sheet: 0.72 (0.44), residues: 150 loop : -0.54 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.002 0.001 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.012 0.002 TYR B 345 ARG 0.004 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 68 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 97 average time/residue: 0.1624 time to fit residues: 24.3269 Evaluate side-chains 86 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9216 Z= 0.286 Angle : 0.557 9.301 12573 Z= 0.295 Chirality : 0.045 0.168 1563 Planarity : 0.004 0.043 1614 Dihedral : 4.252 17.360 1431 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.65 % Allowed : 10.30 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1209 helix: 2.90 (0.23), residues: 516 sheet: 0.72 (0.46), residues: 144 loop : -0.71 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.002 0.001 HIS A 253 PHE 0.008 0.001 PHE C 277 TYR 0.019 0.002 TYR A 427 ARG 0.001 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 71 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 TYR cc_start: 0.7300 (t80) cc_final: 0.7069 (t80) outliers start: 42 outliers final: 32 residues processed: 107 average time/residue: 0.2018 time to fit residues: 31.2190 Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 63 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 115 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9216 Z= 0.207 Angle : 0.526 9.213 12573 Z= 0.277 Chirality : 0.044 0.187 1563 Planarity : 0.004 0.042 1614 Dihedral : 4.156 16.870 1431 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.10 % Allowed : 11.18 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1209 helix: 3.07 (0.23), residues: 516 sheet: 0.69 (0.47), residues: 144 loop : -0.69 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.001 0.000 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.020 0.001 TYR A 427 ARG 0.007 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 70 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8730 (tp) cc_final: 0.8494 (tp) REVERT: C 345 TYR cc_start: 0.7250 (t80) cc_final: 0.7012 (t80) REVERT: C 446 ILE cc_start: 0.8175 (mm) cc_final: 0.7803 (mt) outliers start: 37 outliers final: 30 residues processed: 101 average time/residue: 0.1913 time to fit residues: 28.3208 Evaluate side-chains 93 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9216 Z= 0.364 Angle : 0.616 8.636 12573 Z= 0.326 Chirality : 0.047 0.169 1563 Planarity : 0.004 0.044 1614 Dihedral : 4.386 16.868 1431 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.54 % Allowed : 12.62 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1209 helix: 2.72 (0.23), residues: 516 sheet: 0.43 (0.46), residues: 144 loop : -0.95 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 303 HIS 0.003 0.001 HIS A 253 PHE 0.010 0.002 PHE C 277 TYR 0.022 0.002 TYR B 427 ARG 0.003 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 68 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 30 residues processed: 95 average time/residue: 0.1599 time to fit residues: 23.7961 Evaluate side-chains 91 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 61 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9216 Z= 0.246 Angle : 0.600 11.595 12573 Z= 0.310 Chirality : 0.046 0.228 1563 Planarity : 0.004 0.043 1614 Dihedral : 4.344 17.559 1431 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.54 % Allowed : 13.40 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1209 helix: 2.90 (0.24), residues: 513 sheet: 0.44 (0.47), residues: 144 loop : -0.87 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 303 HIS 0.001 0.001 HIS B 253 PHE 0.008 0.001 PHE B 277 TYR 0.020 0.002 TYR A 379 ARG 0.002 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 63 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 446 ILE cc_start: 0.8176 (mm) cc_final: 0.7819 (mt) outliers start: 32 outliers final: 31 residues processed: 91 average time/residue: 0.1618 time to fit residues: 23.0968 Evaluate side-chains 90 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 59 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 95 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9216 Z= 0.167 Angle : 0.553 10.354 12573 Z= 0.285 Chirality : 0.044 0.150 1563 Planarity : 0.004 0.045 1614 Dihedral : 4.137 16.754 1431 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.88 % Allowed : 14.06 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1209 helix: 3.12 (0.24), residues: 516 sheet: 0.56 (0.48), residues: 144 loop : -0.85 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE C 230 TYR 0.023 0.001 TYR B 427 ARG 0.001 0.000 ARG A 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 446 ILE cc_start: 0.8231 (mm) cc_final: 0.7970 (mt) REVERT: C 446 ILE cc_start: 0.8176 (mm) cc_final: 0.7872 (mt) outliers start: 26 outliers final: 25 residues processed: 90 average time/residue: 0.1577 time to fit residues: 22.2531 Evaluate side-chains 85 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135692 restraints weight = 11561.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122162 restraints weight = 22491.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121652 restraints weight = 19482.430| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.192 Angle : 0.551 10.574 12573 Z= 0.283 Chirality : 0.044 0.156 1563 Planarity : 0.004 0.045 1614 Dihedral : 4.081 17.017 1431 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.99 % Allowed : 14.95 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1209 helix: 3.10 (0.23), residues: 516 sheet: 0.63 (0.48), residues: 144 loop : -0.86 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 253 PHE 0.008 0.001 PHE C 230 TYR 0.031 0.002 TYR C 427 ARG 0.001 0.000 ARG A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2045.14 seconds wall clock time: 37 minutes 42.55 seconds (2262.55 seconds total)