Starting phenix.real_space_refine on Fri Nov 15 15:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/11_2024/8tve_41639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/11_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_41639/11_2024/8tve_41639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/11_2024/8tve_41639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/11_2024/8tve_41639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/11_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. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9090 Number of models: 1 Model: "" Number of chains: 2 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: "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 Restraints were copied for chains: C, B Time building chain proxies: 8.18, per 1000 atoms: 0.90 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=5, 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 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 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 3.07 Time building geometry restraints manager: 2.65 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: 0.00 - 2.28: 11244 2.28 - 4.56: 1059 4.56 - 6.85: 225 6.85 - 9.13: 33 9.13 - 11.41: 12 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 - 16.37: 5447 16.37 - 32.75: 171 32.75 - 49.12: 23 49.12 - 65.50: 19 65.50 - 81.87: 10 Dihedral angle restraints: 5670 sinusoidal: 2088 harmonic: 3582 Sorted by residual: 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 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -129.08 43.08 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -117.49 31.49 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 5667 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: 2.02 - 2.60: 40 2.60 - 3.17: 7716 3.17 - 3.75: 12893 3.75 - 4.32: 18017 4.32 - 4.90: 29475 Nonbonded interactions: 68141 Sorted by model distance: nonbonded pdb=" SG CYS C 350 " pdb=" SG CYS C 358 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS B 350 " pdb=" SG CYS B 358 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS B 382 " pdb=" SG CYS B 387 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 382 " pdb=" SG CYS C 387 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 326 " pdb=" SG CYS C 335 " model vdw 2.036 3.760 ... (remaining 68136 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: 15.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- 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= 0.841 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 : 2.020 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 to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.964 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: 0.2718 time to fit residues: 56.6552 Evaluate side-chains 85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 0.8980 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 279 ASN C 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9216 Z= 0.216 Angle : 0.599 6.488 12573 Z= 0.333 Chirality : 0.045 0.141 1563 Planarity : 0.004 0.028 1614 Dihedral : 4.877 20.310 1431 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.44 % Allowed : 6.42 % Favored : 91.14 % 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: 1.64 (0.23), residues: 1209 helix: 2.61 (0.23), residues: 510 sheet: 0.62 (0.39), residues: 150 loop : -0.24 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 303 HIS 0.001 0.000 HIS C 24 PHE 0.013 0.002 PHE C 209 TYR 0.018 0.002 TYR C 427 ARG 0.004 0.001 ARG C 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 111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.023 Fit side-chains REVERT: B 217 VAL cc_start: 0.9001 (t) cc_final: 0.8747 (m) REVERT: C 427 TYR cc_start: 0.8361 (t80) cc_final: 0.8145 (t80) outliers start: 22 outliers final: 8 residues processed: 102 average time/residue: 0.1791 time to fit residues: 27.3869 Evaluate side-chains 77 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.0040 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- 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: 0.7857 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9216 Z= 0.194 Angle : 0.522 5.847 12573 Z= 0.287 Chirality : 0.044 0.141 1563 Planarity : 0.003 0.034 1614 Dihedral : 4.354 18.492 1431 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 8.08 % Favored : 88.93 % 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: 1.96 (0.24), residues: 1209 helix: 3.13 (0.24), residues: 510 sheet: 0.71 (0.40), residues: 150 loop : -0.32 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 303 HIS 0.001 0.000 HIS C 24 PHE 0.009 0.001 PHE B 277 TYR 0.016 0.001 TYR C 427 ARG 0.003 0.000 ARG C 388 *********************** 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 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.034 Fit side-chains REVERT: B 217 VAL cc_start: 0.9089 (t) cc_final: 0.8751 (m) REVERT: B 388 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7974 (mtm-85) REVERT: B 447 ASP cc_start: 0.8119 (m-30) cc_final: 0.7908 (m-30) REVERT: B 467 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7006 (t0) REVERT: C 427 TYR cc_start: 0.8283 (t80) cc_final: 0.7953 (t80) outliers start: 27 outliers final: 16 residues processed: 99 average time/residue: 0.2010 time to fit residues: 29.0421 Evaluate side-chains 83 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 469 ILE 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 467 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9216 Z= 0.280 Angle : 0.567 6.563 12573 Z= 0.307 Chirality : 0.046 0.155 1563 Planarity : 0.004 0.039 1614 Dihedral : 4.338 18.004 1431 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.10 % Allowed : 9.19 % Favored : 86.71 % 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: 1.66 (0.24), residues: 1209 helix: 2.80 (0.23), residues: 513 sheet: 0.63 (0.42), residues: 150 loop : -0.45 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 303 HIS 0.003 0.001 HIS B 253 PHE 0.008 0.002 PHE A 310 TYR 0.015 0.002 TYR C 427 ARG 0.002 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 110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.990 Fit side-chains REVERT: A 185 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6730 (tt) REVERT: C 233 ASN cc_start: 0.8811 (t0) cc_final: 0.8607 (t0) REVERT: C 424 VAL cc_start: 0.8166 (t) cc_final: 0.7963 (p) outliers start: 37 outliers final: 21 residues processed: 105 average time/residue: 0.2022 time to fit residues: 30.3750 Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL 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 363 VAL 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 262 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 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: 0.2980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 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: 0.7947 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9216 Z= 0.242 Angle : 0.529 5.811 12573 Z= 0.283 Chirality : 0.044 0.151 1563 Planarity : 0.004 0.043 1614 Dihedral : 4.236 17.519 1431 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.54 % Allowed : 10.41 % Favored : 86.05 % 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: 1.65 (0.24), residues: 1209 helix: 2.92 (0.24), residues: 516 sheet: 0.57 (0.44), residues: 150 loop : -0.60 (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 0.006 0.001 PHE A 310 TYR 0.022 0.002 TYR B 427 ARG 0.004 0.001 ARG B 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 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.7064 (t0) REVERT: C 424 VAL cc_start: 0.8242 (t) cc_final: 0.7988 (p) outliers start: 32 outliers final: 19 residues processed: 101 average time/residue: 0.1921 time to fit residues: 28.6488 Evaluate side-chains 86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 363 VAL Chi-restraints excluded: chain A residue 406 LEU 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 167 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 467 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 389 CYS 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: 0.0970 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9216 Z= 0.240 Angle : 0.529 6.365 12573 Z= 0.281 Chirality : 0.044 0.138 1563 Planarity : 0.004 0.042 1614 Dihedral : 4.188 17.134 1431 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.54 % Allowed : 12.29 % Favored : 84.16 % 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: 1.64 (0.24), residues: 1209 helix: 2.97 (0.23), residues: 516 sheet: 0.70 (0.46), residues: 144 loop : -0.70 (0.23), residues: 549 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 0.018 0.002 TYR A 427 ARG 0.003 0.000 ARG B 388 *********************** 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 103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 98 average time/residue: 0.2164 time to fit residues: 30.0613 Evaluate side-chains 85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9216 Z= 0.186 Angle : 0.504 9.208 12573 Z= 0.265 Chirality : 0.043 0.155 1563 Planarity : 0.004 0.049 1614 Dihedral : 4.066 17.025 1431 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 2.77 % Allowed : 13.62 % Favored : 83.61 % 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: 1.78 (0.25), residues: 1209 helix: 3.15 (0.24), residues: 516 sheet: 0.76 (0.47), residues: 144 loop : -0.70 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 PHE 0.007 0.001 PHE C 277 TYR 0.033 0.002 TYR C 427 ARG 0.004 0.000 ARG A 220 *********************** 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 102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8720 (tp) cc_final: 0.8499 (tp) REVERT: C 388 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.7913 (mtm-85) outliers start: 25 outliers final: 20 residues processed: 98 average time/residue: 0.2054 time to fit residues: 29.4853 Evaluate side-chains 84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 469 ILE Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 167 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.5514 ------------------------------------------------------------------------------- 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: 0.7964 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9216 Z= 0.260 Angle : 0.541 8.775 12573 Z= 0.285 Chirality : 0.045 0.167 1563 Planarity : 0.004 0.045 1614 Dihedral : 4.120 16.879 1431 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 3.32 % Allowed : 14.06 % Favored : 82.61 % 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 (0.25), residues: 1209 helix: 3.06 (0.23), residues: 516 sheet: 0.63 (0.47), residues: 144 loop : -0.82 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.002 0.001 HIS B 253 PHE 0.009 0.001 PHE C 277 TYR 0.016 0.002 TYR B 379 ARG 0.005 0.000 ARG B 388 *********************** 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 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8776 (tp) cc_final: 0.8552 (tp) outliers start: 30 outliers final: 28 residues processed: 92 average time/residue: 0.1867 time to fit residues: 27.0258 Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 59 ASN Chi-restraints excluded: chain B residue 153 VAL 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 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 158 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 266 VAL 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: 0.2980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9216 Z= 0.213 Angle : 0.521 8.806 12573 Z= 0.273 Chirality : 0.044 0.160 1563 Planarity : 0.004 0.044 1614 Dihedral : 4.094 16.850 1431 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 3.10 % Allowed : 14.51 % Favored : 82.39 % 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: 1.68 (0.25), residues: 1209 helix: 3.19 (0.23), residues: 516 sheet: 0.64 (0.47), residues: 144 loop : -0.87 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.023 0.002 TYR A 427 ARG 0.005 0.000 ARG B 388 *********************** 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 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8764 (tp) cc_final: 0.8545 (tp) outliers start: 28 outliers final: 25 residues processed: 93 average time/residue: 0.1734 time to fit residues: 24.6999 Evaluate side-chains 88 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 59 ASN 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 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 389 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 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 95 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9216 Z= 0.210 Angle : 0.519 8.727 12573 Z= 0.271 Chirality : 0.044 0.162 1563 Planarity : 0.004 0.044 1614 Dihedral : 4.049 16.784 1431 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.31 % Favored : 96.53 % Rotamer: Outliers : 2.99 % Allowed : 14.62 % Favored : 82.39 % 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: 1.69 (0.25), residues: 1209 helix: 3.21 (0.23), residues: 516 sheet: 0.63 (0.47), residues: 144 loop : -0.87 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 PHE 0.008 0.001 PHE B 277 TYR 0.023 0.001 TYR C 427 ARG 0.004 0.000 ARG B 388 ********************** 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 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.940 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 25 residues processed: 88 average time/residue: 0.1606 time to fit residues: 22.2444 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 59 ASN 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 205 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 389 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: 0.7980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.0010 chunk 95 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.0070 chunk 83 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123661 restraints weight = 11409.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121152 restraints weight = 15052.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122054 restraints weight = 15732.419| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9216 Z= 0.163 Angle : 0.529 10.591 12573 Z= 0.273 Chirality : 0.044 0.209 1563 Planarity : 0.004 0.044 1614 Dihedral : 4.009 16.905 1431 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.36 % Rotamer: Outliers : 2.66 % Allowed : 15.50 % Favored : 81.84 % 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: 1.80 (0.25), residues: 1209 helix: 3.31 (0.23), residues: 516 sheet: 0.68 (0.48), residues: 144 loop : -0.83 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 303 HIS 0.000 0.000 HIS B 24 PHE 0.008 0.001 PHE C 230 TYR 0.023 0.001 TYR A 427 ARG 0.005 0.000 ARG B 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.04 seconds wall clock time: 40 minutes 6.52 seconds (2406.52 seconds total)