Starting phenix.real_space_refine on Mon May 12 16:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_41639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_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/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_41639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_41639.map" model { file = "/net/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_41639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tve_41639/05_2025/8tve_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-5687/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: 7.63, per 1000 atoms: 0.84 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 C 66 " - pdb=" SG CYS C 187 " distance=2.06 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.06 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 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: 2.26 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: 1.19 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: 2.97 Time building geometry restraints manager: 2.66 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 - 16.38: 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 13.700 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: 0.000 Set scattering table: 0.000 Process input model: 24.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- 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 9237 Z= 0.713 Angle : 1.541 11.571 12621 Z= 1.078 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 Details of bonding type rmsd link_NAG-ASN : bond 0.06274 ( 6) link_NAG-ASN : angle 2.01855 ( 18) hydrogen bonds : bond 0.20863 ( 547) hydrogen bonds : angle 7.56919 ( 1530) SS BOND : bond 0.01491 ( 15) SS BOND : angle 5.16874 ( 30) covalent geometry : bond 0.01280 ( 9216) covalent geometry : angle 1.52164 (12573) *********************** 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 : 0.949 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: 0.2521 time to fit residues: 52.4899 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 : 0.940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125571 restraints weight = 11238.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124537 restraints weight = 14222.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126264 restraints weight = 11643.928| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 9237 Z= 0.152 Angle : 0.593 6.324 12621 Z= 0.327 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 6) link_NAG-ASN : angle 1.49239 ( 18) hydrogen bonds : bond 0.05719 ( 547) hydrogen bonds : angle 4.84746 ( 1530) SS BOND : bond 0.00176 ( 15) SS BOND : angle 1.55477 ( 30) covalent geometry : bond 0.00331 ( 9216) covalent geometry : angle 0.58643 (12573) *********************** 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 to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.010 Fit side-chains REVERT: B 217 VAL cc_start: 0.9053 (t) cc_final: 0.8788 (m) REVERT: B 447 ASP cc_start: 0.8092 (m-30) cc_final: 0.7857 (m-30) REVERT: C 427 TYR cc_start: 0.8314 (t80) cc_final: 0.8053 (t80) outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 0.1769 time to fit residues: 27.9133 Evaluate side-chains 72 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** C 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120572 restraints weight = 11450.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120207 restraints weight = 11113.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120324 restraints weight = 10395.020| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9237 Z= 0.204 Angle : 0.607 6.844 12621 Z= 0.333 Chirality : 0.047 0.151 1563 Planarity : 0.004 0.035 1614 Dihedral : 4.499 17.734 1431 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.88 % Allowed : 7.86 % Favored : 88.26 % 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: 1.51 (0.23), residues: 1209 helix: 2.68 (0.23), residues: 513 sheet: 0.52 (0.41), residues: 150 loop : -0.50 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 303 HIS 0.003 0.001 HIS B 253 PHE 0.010 0.002 PHE A 310 TYR 0.017 0.002 TYR C 427 ARG 0.002 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 1.75458 ( 18) hydrogen bonds : bond 0.05155 ( 547) hydrogen bonds : angle 4.56808 ( 1530) SS BOND : bond 0.00213 ( 15) SS BOND : angle 0.91669 ( 30) covalent geometry : bond 0.00512 ( 9216) covalent geometry : angle 0.60263 (12573) *********************** 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 to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 233 ASN cc_start: 0.8640 (t0) cc_final: 0.8409 (t0) REVERT: C 233 ASN cc_start: 0.8779 (t0) cc_final: 0.8458 (t0) outliers start: 35 outliers final: 22 residues processed: 104 average time/residue: 0.1922 time to fit residues: 28.9483 Evaluate side-chains 86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 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 363 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 116 optimal weight: 0.0980 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135164 restraints weight = 11266.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124501 restraints weight = 15992.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124372 restraints weight = 13438.250| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9237 Z= 0.140 Angle : 0.519 6.099 12621 Z= 0.280 Chirality : 0.044 0.136 1563 Planarity : 0.004 0.041 1614 Dihedral : 4.288 17.442 1431 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.32 % Allowed : 8.86 % Favored : 87.82 % 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 (0.24), residues: 1209 helix: 2.93 (0.24), residues: 513 sheet: 0.52 (0.43), residues: 150 loop : -0.51 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 303 HIS 0.001 0.001 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.021 0.001 TYR A 427 ARG 0.002 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 6) link_NAG-ASN : angle 1.41650 ( 18) hydrogen bonds : bond 0.04226 ( 547) hydrogen bonds : angle 4.17920 ( 1530) SS BOND : bond 0.00196 ( 15) SS BOND : angle 0.93631 ( 30) covalent geometry : bond 0.00337 ( 9216) covalent geometry : angle 0.51502 (12573) *********************** 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 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 102 average time/residue: 0.1974 time to fit residues: 30.0193 Evaluate side-chains 79 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 357 LYS 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 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 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 64 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123189 restraints weight = 11447.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122767 restraints weight = 11934.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122587 restraints weight = 12588.170| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9237 Z= 0.160 Angle : 0.544 7.813 12621 Z= 0.289 Chirality : 0.045 0.178 1563 Planarity : 0.004 0.041 1614 Dihedral : 4.246 17.333 1431 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.43 % Allowed : 11.07 % Favored : 85.49 % 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: 2.88 (0.23), residues: 516 sheet: 0.80 (0.45), residues: 144 loop : -0.60 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.001 0.001 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.018 0.002 TYR B 427 ARG 0.005 0.001 ARG C 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 6) link_NAG-ASN : angle 1.43114 ( 18) hydrogen bonds : bond 0.04248 ( 547) hydrogen bonds : angle 4.18133 ( 1530) SS BOND : bond 0.00185 ( 15) SS BOND : angle 0.68630 ( 30) covalent geometry : bond 0.00401 ( 9216) covalent geometry : angle 0.54111 (12573) *********************** 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 95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASN cc_start: 0.8690 (t0) cc_final: 0.8476 (t0) REVERT: C 233 ASN cc_start: 0.8822 (t0) cc_final: 0.8574 (t0) outliers start: 31 outliers final: 20 residues processed: 91 average time/residue: 0.1543 time to fit residues: 22.1397 Evaluate side-chains 83 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 215 ASN Chi-restraints excluded: chain B residue 262 ILE 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 C residue 158 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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** A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131659 restraints weight = 11370.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120598 restraints weight = 20807.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119378 restraints weight = 17382.385| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9237 Z= 0.157 Angle : 0.543 9.280 12621 Z= 0.285 Chirality : 0.044 0.158 1563 Planarity : 0.004 0.040 1614 Dihedral : 4.216 17.355 1431 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.65 % Allowed : 12.18 % 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: 1.61 (0.24), residues: 1209 helix: 2.94 (0.23), residues: 516 sheet: 0.76 (0.46), residues: 144 loop : -0.75 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.001 0.001 HIS B 253 PHE 0.008 0.001 PHE C 277 TYR 0.015 0.002 TYR A 427 ARG 0.002 0.000 ARG C 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 6) link_NAG-ASN : angle 1.44326 ( 18) hydrogen bonds : bond 0.04193 ( 547) hydrogen bonds : angle 4.16176 ( 1530) SS BOND : bond 0.00172 ( 15) SS BOND : angle 0.52572 ( 30) covalent geometry : bond 0.00392 ( 9216) covalent geometry : angle 0.54111 (12573) *********************** 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 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8562 (m110) REVERT: B 233 ASN cc_start: 0.8771 (t0) cc_final: 0.8528 (t0) REVERT: C 233 ASN cc_start: 0.8877 (t0) cc_final: 0.8604 (t0) outliers start: 33 outliers final: 27 residues processed: 102 average time/residue: 0.1981 time to fit residues: 28.8497 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 : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 ASN Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS 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 166 VAL 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 348 ILE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 389 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 205 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 93 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.138377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118560 restraints weight = 11670.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117491 restraints weight = 12869.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117585 restraints weight = 13326.060| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9237 Z= 0.214 Angle : 0.605 10.625 12621 Z= 0.317 Chirality : 0.046 0.163 1563 Planarity : 0.004 0.045 1614 Dihedral : 4.359 17.112 1431 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.99 % Allowed : 12.51 % Favored : 83.50 % 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: 1.33 (0.24), residues: 1209 helix: 2.78 (0.23), residues: 513 sheet: 0.84 (0.48), residues: 135 loop : -1.00 (0.22), residues: 561 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 0.009 0.002 PHE B 277 TYR 0.020 0.002 TYR B 427 ARG 0.002 0.000 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 6) link_NAG-ASN : angle 1.65514 ( 18) hydrogen bonds : bond 0.04622 ( 547) hydrogen bonds : angle 4.34943 ( 1530) SS BOND : bond 0.00231 ( 15) SS BOND : angle 0.57301 ( 30) covalent geometry : bond 0.00552 ( 9216) covalent geometry : angle 0.60233 (12573) *********************** 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: 36 poor density : 66 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 ASN cc_start: 0.8839 (t0) cc_final: 0.8617 (t0) REVERT: C 233 ASN cc_start: 0.8923 (t0) cc_final: 0.8653 (t0) REVERT: C 446 ILE cc_start: 0.8366 (mm) cc_final: 0.7951 (mt) outliers start: 36 outliers final: 30 residues processed: 96 average time/residue: 0.1528 time to fit residues: 22.9929 Evaluate side-chains 92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 298 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 389 CYS 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 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 298 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 158 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 ILE 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 357 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 0.0010 chunk 93 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.140231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120552 restraints weight = 11792.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120383 restraints weight = 12253.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120340 restraints weight = 11995.194| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9237 Z= 0.166 Angle : 0.577 9.958 12621 Z= 0.300 Chirality : 0.045 0.219 1563 Planarity : 0.004 0.044 1614 Dihedral : 4.320 17.247 1431 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.88 % Allowed : 12.74 % Favored : 83.39 % 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: 1.37 (0.24), residues: 1209 helix: 2.90 (0.24), residues: 513 sheet: 0.48 (0.47), residues: 144 loop : -0.97 (0.23), residues: 552 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 0.008 0.001 PHE C 277 TYR 0.017 0.002 TYR B 379 ARG 0.002 0.000 ARG C 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 6) link_NAG-ASN : angle 1.54407 ( 18) hydrogen bonds : bond 0.04360 ( 547) hydrogen bonds : angle 4.23858 ( 1530) SS BOND : bond 0.00201 ( 15) SS BOND : angle 1.33272 ( 30) covalent geometry : bond 0.00416 ( 9216) covalent geometry : angle 0.57100 (12573) *********************** 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 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 ASN cc_start: 0.8900 (t0) cc_final: 0.8642 (t0) REVERT: C 446 ILE cc_start: 0.8380 (mm) cc_final: 0.7966 (mt) outliers start: 35 outliers final: 32 residues processed: 96 average time/residue: 0.1726 time to fit residues: 25.3931 Evaluate side-chains 92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 ILE 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 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 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 298 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 66 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 THR 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 298 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 16 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 28 optimal weight: 0.0980 chunk 41 optimal weight: 0.0770 chunk 103 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.1294 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.145869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136767 restraints weight = 11559.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126405 restraints weight = 19848.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124651 restraints weight = 16900.235| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9237 Z= 0.107 Angle : 0.539 9.371 12621 Z= 0.278 Chirality : 0.043 0.232 1563 Planarity : 0.004 0.042 1614 Dihedral : 4.115 16.925 1431 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 14.51 % Favored : 83.28 % 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: 1.67 (0.25), residues: 1209 helix: 3.17 (0.24), residues: 516 sheet: 0.69 (0.48), residues: 144 loop : -0.88 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 303 HIS 0.001 0.001 HIS C 253 PHE 0.011 0.001 PHE C 230 TYR 0.022 0.001 TYR B 427 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 6) link_NAG-ASN : angle 1.72858 ( 18) hydrogen bonds : bond 0.03618 ( 547) hydrogen bonds : angle 3.90436 ( 1530) SS BOND : bond 0.00224 ( 15) SS BOND : angle 2.10659 ( 30) covalent geometry : bond 0.00219 ( 9216) covalent geometry : angle 0.52613 (12573) *********************** 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 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 ASN cc_start: 0.8858 (t0) cc_final: 0.8640 (t0) REVERT: C 446 ILE cc_start: 0.8355 (mm) cc_final: 0.8000 (mt) outliers start: 20 outliers final: 19 residues processed: 87 average time/residue: 0.1590 time to fit residues: 21.4973 Evaluate side-chains 80 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 348 ILE 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 205 ILE Chi-restraints excluded: chain B residue 215 ASN 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 205 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 63 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.139693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131439 restraints weight = 11883.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119018 restraints weight = 20999.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115859 restraints weight = 29350.268| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9237 Z= 0.198 Angle : 0.620 9.928 12621 Z= 0.321 Chirality : 0.046 0.168 1563 Planarity : 0.004 0.047 1614 Dihedral : 4.282 17.213 1431 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.66 % Allowed : 15.17 % Favored : 82.17 % 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: 1.34 (0.24), residues: 1209 helix: 2.89 (0.23), residues: 513 sheet: 0.50 (0.48), residues: 144 loop : -1.02 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 303 HIS 0.003 0.001 HIS B 253 PHE 0.009 0.001 PHE B 277 TYR 0.027 0.002 TYR A 427 ARG 0.002 0.000 ARG A 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 6) link_NAG-ASN : angle 1.73633 ( 18) hydrogen bonds : bond 0.04317 ( 547) hydrogen bonds : angle 4.21229 ( 1530) SS BOND : bond 0.00291 ( 15) SS BOND : angle 2.13848 ( 30) covalent geometry : bond 0.00510 ( 9216) covalent geometry : angle 0.60857 (12573) ********************** 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 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 ASN cc_start: 0.8952 (t0) cc_final: 0.8748 (t0) REVERT: C 446 ILE cc_start: 0.8447 (mm) cc_final: 0.8036 (mt) outliers start: 24 outliers final: 23 residues processed: 84 average time/residue: 0.1645 time to fit residues: 21.8172 Evaluate side-chains 84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 167 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 348 ILE 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 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 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 205 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 298 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 29 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.142639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123041 restraints weight = 11710.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122462 restraints weight = 13914.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122510 restraints weight = 13558.266| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9237 Z= 0.134 Angle : 0.587 9.941 12621 Z= 0.301 Chirality : 0.045 0.204 1563 Planarity : 0.004 0.045 1614 Dihedral : 4.219 16.783 1431 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.55 % Allowed : 15.84 % Favored : 81.62 % 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: 1.50 (0.25), residues: 1209 helix: 3.03 (0.24), residues: 513 sheet: 0.54 (0.49), residues: 144 loop : -0.93 (0.23), residues: 552 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 230 TYR 0.031 0.002 TYR C 427 ARG 0.003 0.000 ARG A 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 1.74323 ( 18) hydrogen bonds : bond 0.03979 ( 547) hydrogen bonds : angle 4.08139 ( 1530) SS BOND : bond 0.00239 ( 15) SS BOND : angle 2.25151 ( 30) covalent geometry : bond 0.00322 ( 9216) covalent geometry : angle 0.57367 (12573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.03 seconds wall clock time: 49 minutes 40.51 seconds (2980.51 seconds total)