Starting phenix.real_space_refine on Wed Sep 25 00:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/09_2024/7zo8_14843.cif" } resolution = 3.6 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= 0.004 sd= 0.120 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5678 2.51 5 N 1582 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8952 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Restraints were copied for chains: B Time building chain proxies: 10.38, per 1000 atoms: 1.16 Number of scatterers: 8952 At special positions: 0 Unit cell: (74.825, 109.675, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1646 8.00 N 1582 7.00 C 5678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 2.1 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 71.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 4.002A pdb=" N TYR A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 48 removed outlier: 3.762A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 100 removed outlier: 3.625A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.949A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 155 through 204 removed outlier: 3.640A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 316 removed outlier: 3.505A pdb=" N PHE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.890A pdb=" N HIS A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.688A pdb=" N VAL A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 4.253A pdb=" N HIS A 442 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.379A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 463 " --> pdb=" O GLY A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 463' Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.002A pdb=" N TYR B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 48 removed outlier: 3.761A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 55 through 100 removed outlier: 3.624A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.950A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 155 through 204 removed outlier: 3.639A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 316 removed outlier: 3.504A pdb=" N PHE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.889A pdb=" N HIS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 removed outlier: 3.689A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 4.252A pdb=" N HIS B 442 " --> pdb=" O HIS B 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.380A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP B 462 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR B 463 " --> pdb=" O GLY B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 463' Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL A 354 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA A 389 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 7.216A pdb=" N VAL A 539 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL B 354 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 340 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 389 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 7.215A pdb=" N VAL B 539 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 541 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1883 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: 2.47 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1470 1.31 - 1.43: 2282 1.43 - 1.55: 5262 1.55 - 1.68: 4 1.68 - 1.80: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C' PLC B 601 " pdb=" O2 PLC B 601 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N PLC A 601 " pdb=" C5 PLC A 601 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12250 3.73 - 7.47: 60 7.47 - 11.20: 4 11.20 - 14.93: 0 14.93 - 18.66: 4 Bond angle restraints: 12318 Sorted by residual: angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 100.95 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PLC B 601 " pdb=" P PLC B 601 " pdb=" O2P PLC B 601 " ideal model delta sigma weight residual 119.61 101.00 18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 110.31 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 110.28 -16.66 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C ARG A 135 " pdb=" N GLN A 136 " pdb=" CA GLN A 136 " ideal model delta sigma weight residual 120.58 114.67 5.91 1.71e+00 3.42e-01 1.20e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 5159 27.06 - 54.11: 283 54.11 - 81.17: 36 81.17 - 108.23: 6 108.23 - 135.28: 6 Dihedral angle restraints: 5490 sinusoidal: 2184 harmonic: 3306 Sorted by residual: dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ASP A 51 " pdb=" CA ASP A 51 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 50 " pdb=" C SER B 50 " pdb=" N ASP B 51 " pdb=" CA ASP B 51 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C3 PLC B 601 " pdb=" C1 PLC B 601 " pdb=" C2 PLC B 601 " pdb=" O3P PLC B 601 " ideal model delta sinusoidal sigma weight residual 67.16 -157.56 -135.28 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 968 0.035 - 0.069: 349 0.069 - 0.104: 79 0.104 - 0.139: 34 0.139 - 0.174: 10 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA PRO A 103 " pdb=" N PRO A 103 " pdb=" C PRO A 103 " pdb=" CB PRO A 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO B 103 " pdb=" N PRO B 103 " pdb=" C PRO B 103 " pdb=" CB PRO B 103 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA HIS B 137 " pdb=" N HIS B 137 " pdb=" C HIS B 137 " pdb=" CB HIS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1437 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C MET B 134 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C MET A 134 " 0.061 2.00e-02 2.50e+03 pdb=" O MET A 134 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 359 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO B 360 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1892 2.79 - 3.31: 9249 3.31 - 3.84: 14444 3.84 - 4.37: 15461 4.37 - 4.90: 28189 Nonbonded interactions: 69235 Sorted by model distance: nonbonded pdb=" OG SER A 490 " pdb=" O ILE A 492 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 490 " pdb=" O ILE B 492 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 561 " pdb=" OG SER B 564 " model vdw 2.319 3.040 nonbonded pdb=" O GLY A 561 " pdb=" OG SER A 564 " model vdw 2.319 3.040 nonbonded pdb=" NH2 ARG A 423 " pdb=" OE2 GLU B 217 " model vdw 2.346 3.120 ... (remaining 69230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) selection = (chain 'B' and (resid 1 through 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) } 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=0.50 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: 4.380 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: 29.280 Find NCS groups from input model: 0.340 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 9104 Z= 0.273 Angle : 0.704 18.665 12318 Z= 0.336 Chirality : 0.041 0.174 1440 Planarity : 0.004 0.057 1572 Dihedral : 16.849 135.282 3350 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.36 % 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: 1.72 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 782 sheet: 0.61 (0.58), residues: 70 loop : -1.58 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.005 0.001 HIS B 137 PHE 0.018 0.001 PHE A 195 TYR 0.007 0.001 TYR A 461 ARG 0.007 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.824 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1585 time to fit residues: 26.9268 Evaluate side-chains 90 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9104 Z= 0.322 Angle : 0.624 8.378 12318 Z= 0.328 Chirality : 0.043 0.182 1440 Planarity : 0.004 0.040 1572 Dihedral : 12.409 130.319 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.49 % Favored : 95.16 % Rotamer: Outliers : 0.85 % Allowed : 7.32 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1140 helix: 1.94 (0.19), residues: 788 sheet: 0.76 (0.57), residues: 70 loop : -1.71 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.007 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.023 0.001 TYR A 263 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.992 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 0.1801 time to fit residues: 27.4450 Evaluate side-chains 97 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 0.0970 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9104 Z= 0.188 Angle : 0.557 9.458 12318 Z= 0.288 Chirality : 0.040 0.164 1440 Planarity : 0.004 0.036 1572 Dihedral : 11.303 113.017 1320 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 0.85 % Allowed : 9.45 % Favored : 89.70 % 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: 1.68 (0.26), residues: 1140 helix: 2.11 (0.19), residues: 782 sheet: 0.74 (0.56), residues: 70 loop : -1.68 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.001 HIS B 137 PHE 0.017 0.001 PHE B 195 TYR 0.022 0.001 TYR A 263 ARG 0.004 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.932 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 97 average time/residue: 0.1564 time to fit residues: 23.3961 Evaluate side-chains 93 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 0.0370 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.261 Angle : 0.581 8.532 12318 Z= 0.300 Chirality : 0.042 0.166 1440 Planarity : 0.004 0.036 1572 Dihedral : 10.424 94.197 1320 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 9.87 % Favored : 88.85 % 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 (0.26), residues: 1140 helix: 2.07 (0.19), residues: 782 sheet: 0.68 (0.56), residues: 70 loop : -1.72 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.006 0.001 HIS A 137 PHE 0.016 0.001 PHE B 195 TYR 0.023 0.001 TYR A 263 ARG 0.002 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.951 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 0.1613 time to fit residues: 23.7397 Evaluate side-chains 96 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9104 Z= 0.282 Angle : 0.596 7.725 12318 Z= 0.306 Chirality : 0.042 0.171 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.874 77.687 1320 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.38 % Allowed : 11.68 % Favored : 86.94 % 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: 1.58 (0.26), residues: 1140 helix: 2.06 (0.19), residues: 780 sheet: 0.78 (0.59), residues: 70 loop : -1.81 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.006 0.001 HIS B 137 PHE 0.017 0.001 PHE A 195 TYR 0.024 0.001 TYR B 263 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.518 Fit side-chains REVERT: B 270 MET cc_start: 0.8458 (ttt) cc_final: 0.8162 (mtp) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.1546 time to fit residues: 22.0724 Evaluate side-chains 95 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9104 Z= 0.358 Angle : 0.640 8.295 12318 Z= 0.330 Chirality : 0.043 0.186 1440 Planarity : 0.004 0.045 1572 Dihedral : 9.640 76.777 1320 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.49 % Allowed : 12.10 % Favored : 86.41 % 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: 1.41 (0.25), residues: 1140 helix: 1.91 (0.19), residues: 780 sheet: 0.75 (0.58), residues: 70 loop : -1.83 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 106 HIS 0.007 0.001 HIS B 137 PHE 0.017 0.002 PHE A 195 TYR 0.026 0.001 TYR A 263 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.977 Fit side-chains REVERT: A 270 MET cc_start: 0.8674 (ttt) cc_final: 0.8298 (mtp) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.1462 time to fit residues: 21.3070 Evaluate side-chains 94 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9104 Z= 0.197 Angle : 0.567 8.506 12318 Z= 0.287 Chirality : 0.040 0.159 1440 Planarity : 0.004 0.036 1572 Dihedral : 8.985 62.842 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 12.63 % Favored : 86.31 % 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: 1.73 (0.26), residues: 1140 helix: 2.15 (0.19), residues: 782 sheet: 0.93 (0.60), residues: 70 loop : -1.71 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 191 PHE 0.017 0.001 PHE A 195 TYR 0.024 0.001 TYR B 263 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.025 Fit side-chains REVERT: A 248 MET cc_start: 0.8354 (mmm) cc_final: 0.7894 (mmm) REVERT: A 270 MET cc_start: 0.8428 (ttt) cc_final: 0.8204 (mtp) REVERT: B 108 GLN cc_start: 0.8465 (mp10) cc_final: 0.7798 (mp10) REVERT: B 248 MET cc_start: 0.8374 (mmm) cc_final: 0.7907 (mmm) outliers start: 6 outliers final: 5 residues processed: 97 average time/residue: 0.1592 time to fit residues: 24.2585 Evaluate side-chains 96 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.263 Angle : 0.592 8.418 12318 Z= 0.301 Chirality : 0.041 0.168 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.859 64.588 1320 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 12.95 % Favored : 85.77 % 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: 1.70 (0.26), residues: 1140 helix: 2.15 (0.19), residues: 780 sheet: 0.85 (0.59), residues: 70 loop : -1.78 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 137 PHE 0.018 0.001 PHE B 195 TYR 0.024 0.001 TYR A 263 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.877 Fit side-chains REVERT: B 108 GLN cc_start: 0.8461 (mp10) cc_final: 0.7740 (mp10) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1752 time to fit residues: 25.1949 Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.218 Angle : 0.583 10.868 12318 Z= 0.293 Chirality : 0.040 0.167 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.712 59.687 1320 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.17 % Allowed : 13.27 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1140 helix: 2.23 (0.19), residues: 780 sheet: 0.86 (0.60), residues: 70 loop : -1.75 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.005 0.001 HIS B 191 PHE 0.018 0.001 PHE B 195 TYR 0.025 0.001 TYR B 263 ARG 0.007 0.000 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8459 (mp10) cc_final: 0.7795 (mp10) REVERT: B 108 GLN cc_start: 0.8445 (mp10) cc_final: 0.7770 (mp10) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 0.1783 time to fit residues: 25.8676 Evaluate side-chains 101 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 104 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9104 Z= 0.170 Angle : 0.558 10.786 12318 Z= 0.278 Chirality : 0.039 0.164 1440 Planarity : 0.004 0.040 1572 Dihedral : 8.350 57.562 1320 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 13.48 % Favored : 85.46 % 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: 2.01 (0.26), residues: 1140 helix: 2.34 (0.19), residues: 784 sheet: 0.93 (0.61), residues: 70 loop : -1.58 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.005 0.001 HIS B 191 PHE 0.015 0.001 PHE A 453 TYR 0.020 0.001 TYR A 263 ARG 0.006 0.000 ARG B 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.852 Fit side-chains REVERT: A 108 GLN cc_start: 0.8394 (mp10) cc_final: 0.7762 (mp10) REVERT: B 108 GLN cc_start: 0.8417 (mp10) cc_final: 0.7810 (mp10) outliers start: 6 outliers final: 6 residues processed: 113 average time/residue: 0.1628 time to fit residues: 27.9307 Evaluate side-chains 109 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.207593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.155056 restraints weight = 27210.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.149940 restraints weight = 31552.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141272 restraints weight = 17951.661| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9104 Z= 0.201 Angle : 0.585 10.565 12318 Z= 0.289 Chirality : 0.040 0.170 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.273 59.052 1320 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.06 % Allowed : 14.54 % Favored : 84.39 % 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: 2.01 (0.26), residues: 1140 helix: 2.37 (0.19), residues: 782 sheet: 0.89 (0.61), residues: 70 loop : -1.62 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS B 191 PHE 0.015 0.001 PHE A 453 TYR 0.023 0.001 TYR B 263 ARG 0.006 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.43 seconds wall clock time: 30 minutes 56.53 seconds (1856.53 seconds total)