Starting phenix.real_space_refine on Fri Sep 11 07:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pur_71874/09_2026/9pur_71874.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.019 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 46 5.16 5 C 5158 2.51 5 N 1372 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8154 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3319 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 399} Chain breaks: 1 Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 688 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain breaks: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: B, I Time building chain proxies: 2.69, per 1000 atoms: 0.33 Number of scatterers: 8154 At special positions: 0 Unit cell: (100.58, 113.74, 80.84, 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 46 16.00 O 1578 8.00 N 1372 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 469 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 469 " distance=2.04 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 544 " distance=2.03 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 173 " " NAG A 602 " - " ASN A 277 " " NAG A 603 " - " ASN A 551 " " NAG A 604 " - " ASN A 361 " " NAG A 605 " - " ASN A 499 " " NAG B 601 " - " ASN B 173 " " NAG B 602 " - " ASN B 277 " " NAG B 603 " - " ASN B 551 " " NAG B 604 " - " ASN B 361 " " NAG B 605 " - " ASN B 499 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 405.4 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.3% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 154 through 159 removed outlier: 4.022A pdb=" N TRP A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'B' and resid 154 through 159 removed outlier: 4.022A pdb=" N TRP B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.780A pdb=" N ALA A 528 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 551 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR A 530 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU A 549 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 557 " --> pdb=" O GLN A 552 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 200 removed outlier: 5.629A pdb=" N SER A 208 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 198 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 206 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN A 224 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 248 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU A 226 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 246 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 228 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 263 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 313 removed outlier: 7.623A pdb=" N LEU A 337 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR A 339 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET A 320 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 341 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 removed outlier: 3.636A pdb=" N ARG A 377 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 412 through 417 removed outlier: 4.844A pdb=" N ILE A 421 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 425 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN A 435 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 481 through 483 Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.779A pdb=" N ALA B 528 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN B 551 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 530 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU B 549 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 557 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'B' and resid 192 through 200 removed outlier: 5.629A pdb=" N SER B 208 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 198 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 206 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 224 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR B 248 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 226 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 246 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 228 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 263 Processing sheet with id=AB6, first strand: chain 'B' and resid 312 through 313 removed outlier: 7.623A pdb=" N LEU B 337 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR B 339 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET B 320 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 341 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 312 through 313 removed outlier: 3.636A pdb=" N ARG B 377 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 412 through 417 removed outlier: 4.843A pdb=" N ILE B 421 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 425 " --> pdb=" O GLN B 435 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN B 435 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 481 through 483 Processing sheet with id=AC1, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AC3, first strand: chain 'H' and resid 69 through 72 Processing sheet with id=AC4, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AC5, first strand: chain 'I' and resid 57 through 59 Processing sheet with id=AC6, first strand: chain 'I' and resid 69 through 72 284 hydrogen bonds defined for protein. 690 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: 1.16 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2582 1.34 - 1.46: 1872 1.46 - 1.58: 3814 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 8330 Sorted by residual: bond pdb=" N ASP B 392 " pdb=" CA ASP B 392 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.44e+00 bond pdb=" N LYS A 395 " pdb=" CA LYS A 395 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.38e+00 bond pdb=" N LYS B 395 " pdb=" CA LYS B 395 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.38e+00 bond pdb=" N ASP A 392 " pdb=" CA ASP A 392 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.33e+00 bond pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.24e-02 6.50e+03 5.43e+00 ... (remaining 8325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 10407 1.25 - 2.50: 752 2.50 - 3.76: 142 3.76 - 5.01: 25 5.01 - 6.26: 6 Bond angle restraints: 11332 Sorted by residual: angle pdb=" CA ASP B 392 " pdb=" CB ASP B 392 " pdb=" CG ASP B 392 " ideal model delta sigma weight residual 112.60 116.29 -3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" CA ASP A 392 " pdb=" CB ASP A 392 " pdb=" CG ASP A 392 " ideal model delta sigma weight residual 112.60 116.26 -3.66 1.00e+00 1.00e+00 1.34e+01 angle pdb=" CA ARG B 502 " pdb=" C ARG B 502 " pdb=" O ARG B 502 " ideal model delta sigma weight residual 122.37 118.21 4.16 1.15e+00 7.56e-01 1.31e+01 angle pdb=" CA ARG A 502 " pdb=" C ARG A 502 " pdb=" O ARG A 502 " ideal model delta sigma weight residual 122.37 118.31 4.06 1.15e+00 7.56e-01 1.24e+01 angle pdb=" N GLY B 524 " pdb=" CA GLY B 524 " pdb=" C GLY B 524 " ideal model delta sigma weight residual 113.76 119.45 -5.69 1.80e+00 3.09e-01 9.99e+00 ... (remaining 11327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4765 17.88 - 35.76: 304 35.76 - 53.63: 51 53.63 - 71.51: 10 71.51 - 89.39: 4 Dihedral angle restraints: 5134 sinusoidal: 2154 harmonic: 2980 Sorted by residual: dihedral pdb=" CB CYS B 463 " pdb=" SG CYS B 463 " pdb=" SG CYS B 473 " pdb=" CB CYS B 473 " ideal model delta sinusoidal sigma weight residual -86.00 -132.26 46.26 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS A 463 " pdb=" SG CYS A 463 " pdb=" SG CYS A 473 " pdb=" CB CYS A 473 " ideal model delta sinusoidal sigma weight residual -86.00 -132.25 46.25 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CG ARG A 305 " pdb=" CD ARG A 305 " pdb=" NE ARG A 305 " pdb=" CZ ARG A 305 " ideal model delta sinusoidal sigma weight residual 180.00 137.10 42.90 2 1.50e+01 4.44e-03 9.88e+00 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 839 0.038 - 0.076: 329 0.076 - 0.115: 122 0.115 - 0.153: 26 0.153 - 0.191: 8 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CB THR B 512 " pdb=" CA THR B 512 " pdb=" OG1 THR B 512 " pdb=" CG2 THR B 512 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CB THR A 512 " pdb=" CA THR A 512 " pdb=" OG1 THR A 512 " pdb=" CG2 THR A 512 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C2 NAG B 605 " pdb=" C1 NAG B 605 " pdb=" C3 NAG B 605 " pdb=" N2 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1321 not shown) Planarity restraints: 1436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 502 " 0.262 9.50e-02 1.11e+02 1.18e-01 8.50e+00 pdb=" NE ARG B 502 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 502 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 502 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 502 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 502 " 0.230 9.50e-02 1.11e+02 1.03e-01 6.53e+00 pdb=" NE ARG A 502 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 502 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 502 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 471 " -0.158 9.50e-02 1.11e+02 7.16e-02 4.07e+00 pdb=" NE ARG A 471 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 471 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 471 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 471 " -0.000 2.00e-02 2.50e+03 ... (remaining 1433 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3313 2.90 - 3.40: 7844 3.40 - 3.90: 13504 3.90 - 4.40: 15622 4.40 - 4.90: 26370 Nonbonded interactions: 66653 Sorted by model distance: nonbonded pdb=" OG SER A 427 " pdb=" O HIS A 431 " model vdw 2.399 3.040 nonbonded pdb=" OG SER B 427 " pdb=" O HIS B 431 " model vdw 2.399 3.040 nonbonded pdb=" O GLY B 264 " pdb=" OG1 THR B 265 " model vdw 2.461 3.040 nonbonded pdb=" O GLY A 264 " pdb=" OG1 THR A 265 " model vdw 2.462 3.040 nonbonded pdb=" O SER B 428 " pdb=" O CYS B 473 " model vdw 2.490 3.040 ... (remaining 66648 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 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 : 0.003 0.034 8354 Z= 0.174 Angle : 0.737 6.262 11390 Z= 0.409 Chirality : 0.048 0.191 1324 Planarity : 0.008 0.118 1426 Dihedral : 11.831 89.389 3188 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.24), residues: 1010 helix: -1.97 (0.62), residues: 30 sheet: -1.65 (0.25), residues: 342 loop : -1.44 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG B 194 TYR 0.012 0.003 TYR A 478 PHE 0.014 0.001 PHE B 313 TRP 0.011 0.001 TRP A 373 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 8330) covalent geometry : angle 0.72902 / 0.41 (11332) SS BOND : bond 0.00245 / 0.17 ( 14) SS BOND : angle 0.84071 / 0.55 ( 28) hydrogen bonds : bond 0.25212 / 16.77 ( 268) hydrogen bonds : angle 11.26394 / 7.65 ( 690) link_NAG-ASN : bond 0.00161 / 0.07 ( 10) link_NAG-ASN : angle 2.18582 / 1.46 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.231 Fit side-chains REVERT: A 256 LYS cc_start: 0.6967 (ttmt) cc_final: 0.6605 (mttp) REVERT: A 307 LYS cc_start: 0.7438 (mmmm) cc_final: 0.7010 (mmmm) REVERT: A 320 MET cc_start: 0.5806 (tmm) cc_final: 0.5563 (tmm) REVERT: A 386 ILE cc_start: 0.7708 (mp) cc_final: 0.7500 (mt) REVERT: A 413 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6773 (tpp80) REVERT: A 435 GLN cc_start: 0.7726 (mp10) cc_final: 0.7374 (mp10) REVERT: B 234 ASN cc_start: 0.5660 (p0) cc_final: 0.5449 (p0) REVERT: B 307 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7183 (mmmm) REVERT: B 435 GLN cc_start: 0.7696 (mp10) cc_final: 0.7378 (mp10) REVERT: B 482 TYR cc_start: 0.7501 (t80) cc_final: 0.7182 (t80) REVERT: B 522 LYS cc_start: 0.7032 (tttt) cc_final: 0.6704 (tttt) REVERT: B 558 PHE cc_start: 0.7853 (m-80) cc_final: 0.7475 (m-80) REVERT: H 71 MET cc_start: 0.5138 (ttt) cc_final: 0.4140 (pmm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1006 time to fit residues: 15.8423 Evaluate side-chains 107 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.187991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.166915 restraints weight = 10821.001| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.54 r_work: 0.4100 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8354 Z= 0.209 Angle : 0.685 6.989 11390 Z= 0.362 Chirality : 0.047 0.169 1324 Planarity : 0.005 0.043 1426 Dihedral : 5.993 57.403 1324 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.09 % Allowed : 9.67 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.24), residues: 1010 helix: -0.82 (0.77), residues: 32 sheet: -1.45 (0.24), residues: 364 loop : -1.44 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 426 TYR 0.013 0.002 TYR A 509 PHE 0.018 0.002 PHE A 313 TRP 0.015 0.002 TRP B 159 HIS 0.006 0.002 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 ( 8330) covalent geometry : angle 0.67855 / 0.36 (11332) SS BOND : bond 0.00403 / 0.27 ( 14) SS BOND : angle 0.98189 / 0.63 ( 28) hydrogen bonds : bond 0.05188 / 3.46 ( 268) hydrogen bonds : angle 8.09225 / 5.46 ( 690) link_NAG-ASN : bond 0.00235 / 0.15 ( 10) link_NAG-ASN : angle 1.89217 / 1.13 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.303 Fit side-chains REVERT: A 307 LYS cc_start: 0.7488 (mmmm) cc_final: 0.7078 (mmmm) REVERT: A 386 ILE cc_start: 0.7602 (mp) cc_final: 0.7379 (mt) REVERT: A 413 ARG cc_start: 0.6828 (tpp80) cc_final: 0.6511 (tpp80) REVERT: B 307 LYS cc_start: 0.7746 (mmmm) cc_final: 0.7300 (mmmm) REVERT: B 386 ILE cc_start: 0.7560 (mp) cc_final: 0.7349 (mt) REVERT: B 558 PHE cc_start: 0.7842 (m-80) cc_final: 0.7435 (m-80) REVERT: H 71 MET cc_start: 0.5142 (ttt) cc_final: 0.4097 (pmm) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.0864 time to fit residues: 13.4472 Evaluate side-chains 114 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 561 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.187521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.165783 restraints weight = 10587.528| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.54 r_work: 0.4111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8354 Z= 0.191 Angle : 0.649 13.718 11390 Z= 0.336 Chirality : 0.046 0.168 1324 Planarity : 0.005 0.044 1426 Dihedral : 5.949 56.082 1324 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.64 % Allowed : 11.65 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.24), residues: 1010 helix: -0.35 (0.83), residues: 32 sheet: -1.48 (0.24), residues: 392 loop : -1.35 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 426 TYR 0.016 0.002 TYR B 482 PHE 0.016 0.002 PHE A 313 TRP 0.023 0.002 TRP B 159 HIS 0.006 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 8330) covalent geometry : angle 0.64230 / 0.33 (11332) SS BOND : bond 0.00334 / 0.22 ( 14) SS BOND : angle 0.88255 / 0.55 ( 28) hydrogen bonds : bond 0.04043 / 2.71 ( 268) hydrogen bonds : angle 7.54139 / 5.09 ( 690) link_NAG-ASN : bond 0.00274 / 0.19 ( 10) link_NAG-ASN : angle 1.87769 / 1.13 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7468 (mmmm) cc_final: 0.7092 (mmmm) REVERT: A 386 ILE cc_start: 0.7598 (mp) cc_final: 0.7379 (mt) REVERT: A 413 ARG cc_start: 0.6920 (tpp80) cc_final: 0.6516 (tpp80) REVERT: B 307 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7262 (mmmm) REVERT: B 413 ARG cc_start: 0.6989 (tpp80) cc_final: 0.6634 (tpp-160) REVERT: B 558 PHE cc_start: 0.7820 (m-80) cc_final: 0.7318 (m-80) REVERT: B 561 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.6035 (mtt) outliers start: 24 outliers final: 11 residues processed: 122 average time/residue: 0.0851 time to fit residues: 14.6431 Evaluate side-chains 113 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 452 HIS B 224 GLN B 452 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.186302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.164022 restraints weight = 10703.549| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.55 r_work: 0.4077 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8354 Z= 0.223 Angle : 0.665 11.870 11390 Z= 0.345 Chirality : 0.047 0.173 1324 Planarity : 0.005 0.045 1426 Dihedral : 6.022 55.349 1324 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.30 % Allowed : 13.52 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.24), residues: 1010 helix: -0.37 (0.83), residues: 32 sheet: -1.54 (0.23), residues: 386 loop : -1.43 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 426 TYR 0.021 0.002 TYR B 482 PHE 0.018 0.002 PHE A 313 TRP 0.028 0.002 TRP B 159 HIS 0.006 0.002 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 8330) covalent geometry : angle 0.65756 / 0.34 (11332) SS BOND : bond 0.00421 / 0.27 ( 14) SS BOND : angle 0.99201 / 0.64 ( 28) hydrogen bonds : bond 0.03937 / 2.67 ( 268) hydrogen bonds : angle 7.42634 / 5.03 ( 690) link_NAG-ASN : bond 0.00308 / 0.20 ( 10) link_NAG-ASN : angle 1.89909 / 1.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7458 (mmmm) cc_final: 0.7090 (mmmm) REVERT: A 413 ARG cc_start: 0.6903 (tpp80) cc_final: 0.6510 (tpp80) REVERT: B 234 ASN cc_start: 0.6038 (p0) cc_final: 0.5828 (p0) REVERT: B 307 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7310 (mmmm) REVERT: I 34 MET cc_start: 0.6206 (ptm) cc_final: 0.5898 (ptm) outliers start: 30 outliers final: 16 residues processed: 123 average time/residue: 0.0824 time to fit residues: 14.3876 Evaluate side-chains 120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 HIS B 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.187188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.165001 restraints weight = 10614.320| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.55 r_work: 0.4096 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8354 Z= 0.178 Angle : 0.629 12.162 11390 Z= 0.324 Chirality : 0.046 0.162 1324 Planarity : 0.005 0.045 1426 Dihedral : 5.922 55.085 1324 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.97 % Allowed : 16.48 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.24), residues: 1010 helix: -0.40 (0.82), residues: 32 sheet: -1.52 (0.24), residues: 366 loop : -1.46 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 426 TYR 0.015 0.002 TYR B 205 PHE 0.016 0.002 PHE A 313 TRP 0.031 0.002 TRP B 159 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 8330) covalent geometry : angle 0.62250 / 0.32 (11332) SS BOND : bond 0.00336 / 0.21 ( 14) SS BOND : angle 0.91384 / 0.59 ( 28) hydrogen bonds : bond 0.03609 / 2.46 ( 268) hydrogen bonds : angle 7.24300 / 4.91 ( 690) link_NAG-ASN : bond 0.00219 / 0.14 ( 10) link_NAG-ASN : angle 1.76864 / 1.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7430 (mmmm) cc_final: 0.7109 (mmmm) REVERT: A 320 MET cc_start: 0.5864 (tmm) cc_final: 0.5573 (tmm) REVERT: A 413 ARG cc_start: 0.6849 (tpp80) cc_final: 0.6444 (tpp80) REVERT: B 234 ASN cc_start: 0.6044 (p0) cc_final: 0.5843 (p0) REVERT: B 307 LYS cc_start: 0.7680 (mmmm) cc_final: 0.7272 (mmmm) REVERT: B 558 PHE cc_start: 0.7833 (m-80) cc_final: 0.7333 (m-80) REVERT: H 66 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4960 (ptt180) REVERT: I 34 MET cc_start: 0.5958 (ptm) cc_final: 0.5712 (ptm) outliers start: 27 outliers final: 18 residues processed: 122 average time/residue: 0.0886 time to fit residues: 15.1100 Evaluate side-chains 119 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 HIS A 464 ASN B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.185852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.164107 restraints weight = 10503.621| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.49 r_work: 0.4088 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8354 Z= 0.204 Angle : 0.648 11.758 11390 Z= 0.334 Chirality : 0.046 0.164 1324 Planarity : 0.005 0.046 1426 Dihedral : 5.952 54.666 1324 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.75 % Allowed : 17.69 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.24), residues: 1010 helix: -1.66 (0.67), residues: 44 sheet: -1.55 (0.25), residues: 330 loop : -1.49 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.020 0.002 TYR A 268 PHE 0.017 0.002 PHE A 313 TRP 0.043 0.002 TRP B 159 HIS 0.006 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 8330) covalent geometry : angle 0.64100 / 0.33 (11332) SS BOND : bond 0.00376 / 0.24 ( 14) SS BOND : angle 0.95509 / 0.60 ( 28) hydrogen bonds : bond 0.03699 / 2.51 ( 268) hydrogen bonds : angle 7.18047 / 4.87 ( 690) link_NAG-ASN : bond 0.00259 / 0.17 ( 10) link_NAG-ASN : angle 1.77408 / 1.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7474 (mmmm) cc_final: 0.7151 (mmmm) REVERT: A 320 MET cc_start: 0.5862 (tmm) cc_final: 0.5544 (tmm) REVERT: A 413 ARG cc_start: 0.6867 (tpp80) cc_final: 0.6462 (tpp80) REVERT: B 307 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7280 (mmmm) REVERT: B 413 ARG cc_start: 0.6938 (tpp80) cc_final: 0.6611 (tpp-160) REVERT: B 558 PHE cc_start: 0.7802 (m-80) cc_final: 0.7273 (m-80) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.0915 time to fit residues: 15.6481 Evaluate side-chains 120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.187889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.166271 restraints weight = 10697.349| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.55 r_work: 0.4105 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8354 Z= 0.126 Angle : 0.589 11.599 11390 Z= 0.302 Chirality : 0.045 0.160 1324 Planarity : 0.005 0.042 1426 Dihedral : 5.673 55.115 1324 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 18.68 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.24), residues: 1010 helix: -0.09 (0.82), residues: 32 sheet: -1.47 (0.25), residues: 330 loop : -1.43 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.016 0.001 TYR A 268 PHE 0.013 0.001 PHE A 313 TRP 0.023 0.001 TRP B 159 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8330) covalent geometry : angle 0.58439 / 0.30 (11332) SS BOND : bond 0.00232 / 0.15 ( 14) SS BOND : angle 0.70570 / 0.44 ( 28) hydrogen bonds : bond 0.03203 / 2.18 ( 268) hydrogen bonds : angle 6.85990 / 4.62 ( 690) link_NAG-ASN : bond 0.00151 / 0.08 ( 10) link_NAG-ASN : angle 1.51781 / 0.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7397 (mmmm) cc_final: 0.7092 (mmmm) REVERT: A 320 MET cc_start: 0.5805 (tmm) cc_final: 0.5559 (tmm) REVERT: A 413 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6422 (tpp80) REVERT: B 384 ILE cc_start: 0.7988 (mt) cc_final: 0.7563 (mt) REVERT: B 413 ARG cc_start: 0.6847 (tpp80) cc_final: 0.6495 (tpp-160) REVERT: B 558 PHE cc_start: 0.7855 (m-80) cc_final: 0.7283 (m-80) outliers start: 24 outliers final: 20 residues processed: 121 average time/residue: 0.0848 time to fit residues: 14.5444 Evaluate side-chains 124 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 GLN B 452 HIS B 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.185166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.162951 restraints weight = 10766.684| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.52 r_work: 0.4071 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8354 Z= 0.250 Angle : 0.678 11.581 11390 Z= 0.350 Chirality : 0.047 0.173 1324 Planarity : 0.006 0.061 1426 Dihedral : 5.955 54.255 1324 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.75 % Allowed : 19.78 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.24), residues: 1010 helix: -1.49 (0.68), residues: 44 sheet: -1.35 (0.25), residues: 350 loop : -1.54 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 305 TYR 0.021 0.002 TYR B 482 PHE 0.020 0.002 PHE B 292 TRP 0.069 0.003 TRP B 159 HIS 0.006 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 ( 8330) covalent geometry : angle 0.67197 / 0.35 (11332) SS BOND : bond 0.00408 / 0.25 ( 14) SS BOND : angle 0.94955 / 0.57 ( 28) hydrogen bonds : bond 0.03886 / 2.63 ( 268) hydrogen bonds : angle 7.14894 / 4.84 ( 690) link_NAG-ASN : bond 0.00298 / 0.20 ( 10) link_NAG-ASN : angle 1.74266 / 1.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7462 (mmmm) cc_final: 0.7135 (mmmm) REVERT: A 413 ARG cc_start: 0.6865 (tpp80) cc_final: 0.6433 (tpp80) REVERT: A 518 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4685 (ppp) REVERT: B 307 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7282 (mmmm) REVERT: B 413 ARG cc_start: 0.6906 (tpp80) cc_final: 0.6512 (tpp-160) REVERT: B 558 PHE cc_start: 0.7915 (m-80) cc_final: 0.7368 (m-80) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.0845 time to fit residues: 14.2569 Evaluate side-chains 128 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 90 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.187808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.165545 restraints weight = 10682.335| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.54 r_work: 0.4103 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8354 Z= 0.158 Angle : 0.616 11.647 11390 Z= 0.317 Chirality : 0.046 0.169 1324 Planarity : 0.005 0.046 1426 Dihedral : 5.810 54.385 1324 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.31 % Allowed : 20.77 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.24), residues: 1010 helix: 0.09 (0.84), residues: 32 sheet: -1.26 (0.25), residues: 350 loop : -1.47 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.016 0.001 TYR A 268 PHE 0.020 0.002 PHE B 292 TRP 0.053 0.002 TRP B 159 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8330) covalent geometry : angle 0.61155 / 0.32 (11332) SS BOND : bond 0.00286 / 0.18 ( 14) SS BOND : angle 0.76781 / 0.47 ( 28) hydrogen bonds : bond 0.03396 / 2.32 ( 268) hydrogen bonds : angle 6.96577 / 4.70 ( 690) link_NAG-ASN : bond 0.00111 / 0.05 ( 10) link_NAG-ASN : angle 1.55562 / 0.94 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7418 (mmmm) cc_final: 0.7132 (mmmm) REVERT: A 413 ARG cc_start: 0.6840 (tpp80) cc_final: 0.6403 (tpp80) REVERT: A 518 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4764 (ppp) REVERT: B 413 ARG cc_start: 0.6908 (tpp80) cc_final: 0.6426 (tpp-160) REVERT: B 558 PHE cc_start: 0.7911 (m-80) cc_final: 0.7426 (m-80) outliers start: 21 outliers final: 19 residues processed: 110 average time/residue: 0.0902 time to fit residues: 13.8211 Evaluate side-chains 118 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.164643 restraints weight = 10707.519| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.52 r_work: 0.4096 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8354 Z= 0.187 Angle : 0.635 11.495 11390 Z= 0.328 Chirality : 0.047 0.169 1324 Planarity : 0.006 0.121 1426 Dihedral : 5.854 54.393 1324 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.42 % Allowed : 20.77 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.24), residues: 1010 helix: 0.19 (0.87), residues: 32 sheet: -1.25 (0.25), residues: 350 loop : -1.49 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 305 TYR 0.015 0.001 TYR A 268 PHE 0.021 0.002 PHE B 292 TRP 0.095 0.003 TRP B 159 HIS 0.006 0.001 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 8330) covalent geometry : angle 0.62965 / 0.33 (11332) SS BOND : bond 0.00332 / 0.20 ( 14) SS BOND : angle 0.80405 / 0.48 ( 28) hydrogen bonds : bond 0.03505 / 2.41 ( 268) hydrogen bonds : angle 6.98472 / 4.72 ( 690) link_NAG-ASN : bond 0.00155 / 0.10 ( 10) link_NAG-ASN : angle 1.59482 / 0.97 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7444 (mmmm) cc_final: 0.7141 (mmmm) REVERT: A 413 ARG cc_start: 0.6858 (tpp80) cc_final: 0.6423 (tpp80) REVERT: B 234 ASN cc_start: 0.6070 (p0) cc_final: 0.5862 (p0) REVERT: B 413 ARG cc_start: 0.6914 (tpp80) cc_final: 0.6423 (tpp-160) REVERT: B 558 PHE cc_start: 0.7919 (m-80) cc_final: 0.7433 (m-80) outliers start: 22 outliers final: 20 residues processed: 110 average time/residue: 0.0900 time to fit residues: 13.8796 Evaluate side-chains 120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 59 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 0.0040 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 435 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.187438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.165179 restraints weight = 10776.508| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.54 r_work: 0.4105 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8354 Z= 0.169 Angle : 0.621 11.482 11390 Z= 0.319 Chirality : 0.046 0.168 1324 Planarity : 0.005 0.046 1426 Dihedral : 5.760 54.008 1324 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.53 % Allowed : 20.55 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.25), residues: 1010 helix: -0.17 (0.83), residues: 32 sheet: -1.20 (0.26), residues: 350 loop : -1.45 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.015 0.001 TYR A 268 PHE 0.019 0.002 PHE B 292 TRP 0.076 0.003 TRP B 159 HIS 0.005 0.001 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 8330) covalent geometry : angle 0.61591 / 0.32 (11332) SS BOND : bond 0.00306 / 0.19 ( 14) SS BOND : angle 0.77242 / 0.46 ( 28) hydrogen bonds : bond 0.03410 / 2.33 ( 268) hydrogen bonds : angle 6.89378 / 4.65 ( 690) link_NAG-ASN : bond 0.00127 / 0.07 ( 10) link_NAG-ASN : angle 1.55709 / 0.95 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.18 seconds wall clock time: 38 minutes 59.78 seconds (2339.78 seconds total)