Starting phenix.real_space_refine on Thu Feb 15 01:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2024/7ou2_13073_neut_updated.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.022 sd= 0.074 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 4 5.49 5 S 54 5.16 5 C 6781 2.51 5 N 1916 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5632 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 33, 'TRANS': 687} Chain breaks: 2 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5112 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 27, 'TRANS': 622} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.17, per 1000 atoms: 0.57 Number of scatterers: 10798 At special positions: 0 Unit cell: (117.66, 99.64, 127.2, 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 54 16.00 P 4 15.00 O 2043 8.00 N 1916 7.00 C 6781 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 48.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 73 through 85 removed outlier: 5.137A pdb=" N GLU A 77 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.650A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 345 removed outlier: 4.585A pdb=" N ASP A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 3.744A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 362 through 384 Proline residue: A 376 - end of helix removed outlier: 3.696A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.815A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 564 removed outlier: 3.618A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Proline residue: A 537 - end of helix removed outlier: 5.074A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.941A pdb=" N MET A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 732 through 738 removed outlier: 3.666A pdb=" N LEU A 735 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Proline residue: A 736 - end of helix No H-bonds generated for 'chain 'A' and resid 732 through 738' Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 73 through 85 removed outlier: 4.991A pdb=" N GLU B 77 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.664A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.521A pdb=" N ARG B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 345 removed outlier: 4.378A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLY B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Proline residue: B 340 - end of helix removed outlier: 3.716A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 362 through 384 Proline residue: B 376 - end of helix removed outlier: 3.619A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 521 through 535 Processing helix chain 'B' and resid 539 through 564 Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 620 through 635 removed outlier: 4.183A pdb=" N MET B 624 " --> pdb=" O LYS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 701 through 717 Processing helix chain 'B' and resid 732 through 738 removed outlier: 3.512A pdb=" N LEU B 735 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Proline residue: B 736 - end of helix No H-bonds generated for 'chain 'B' and resid 732 through 738' Processing helix chain 'B' and resid 771 through 777 Processing helix chain 'B' and resid 783 through 799 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.388A pdb=" N ILE A 66 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 32 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN A 95 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.614A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 571 through 573 removed outlier: 3.980A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 723 through 726 Processing sheet with id= E, first strand: chain 'A' and resid 652 through 657 Processing sheet with id= F, first strand: chain 'A' and resid 749 through 752 Processing sheet with id= G, first strand: chain 'B' and resid 28 through 31 Processing sheet with id= H, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.803A pdb=" N ILE B 71 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.622A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 134 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 571 through 573 removed outlier: 3.843A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 723 through 726 Processing sheet with id= L, first strand: chain 'B' and resid 652 through 656 Processing sheet with id= M, first strand: chain 'B' and resid 750 through 752 506 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 4.51 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: 1839 1.31 - 1.43: 2689 1.43 - 1.56: 6346 1.56 - 1.69: 6 1.69 - 1.82: 96 Bond restraints: 10976 Sorted by residual: bond pdb=" C4 ADP A1801 " pdb=" C5 ADP A1801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C4 ADP B1801 " pdb=" C5 ADP B1801 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta sigma weight residual 1.453 1.495 -0.042 8.30e-03 1.45e+04 2.51e+01 bond pdb=" N ARG B 199 " pdb=" CA ARG B 199 " ideal model delta sigma weight residual 1.453 1.493 -0.040 8.30e-03 1.45e+04 2.30e+01 bond pdb=" C PRO B 615 " pdb=" O PRO B 615 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.19e-02 7.06e+03 2.21e+01 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.09: 389 106.09 - 113.20: 5514 113.20 - 120.31: 5150 120.31 - 127.42: 3746 127.42 - 134.53: 70 Bond angle restraints: 14869 Sorted by residual: angle pdb=" N CYS B 297 " pdb=" CA CYS B 297 " pdb=" C CYS B 297 " ideal model delta sigma weight residual 111.56 101.89 9.67 1.38e+00 5.25e-01 4.91e+01 angle pdb=" N CYS A 297 " pdb=" CA CYS A 297 " pdb=" C CYS A 297 " ideal model delta sigma weight residual 111.71 102.87 8.84 1.34e+00 5.57e-01 4.35e+01 angle pdb=" C THR B 669 " pdb=" CA THR B 669 " pdb=" CB THR B 669 " ideal model delta sigma weight residual 110.88 101.06 9.82 1.57e+00 4.06e-01 3.91e+01 angle pdb=" N ARG A 697 " pdb=" CA ARG A 697 " pdb=" C ARG A 697 " ideal model delta sigma weight residual 112.93 106.08 6.85 1.12e+00 7.97e-01 3.74e+01 angle pdb=" N ILE A 636 " pdb=" CA ILE A 636 " pdb=" C ILE A 636 " ideal model delta sigma weight residual 112.80 105.92 6.88 1.15e+00 7.56e-01 3.58e+01 ... (remaining 14864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 6456 26.73 - 53.45: 244 53.45 - 80.18: 26 80.18 - 106.91: 3 106.91 - 133.63: 3 Dihedral angle restraints: 6732 sinusoidal: 2754 harmonic: 3978 Sorted by residual: dihedral pdb=" O2A ADP A1801 " pdb=" O3A ADP A1801 " pdb=" PA ADP A1801 " pdb=" PB ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 73.64 -133.63 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O2A ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PA ADP B1801 " pdb=" PB ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 60.77 -120.77 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" O1B ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PB ADP B1801 " pdb=" PA ADP B1801 " ideal model delta sinusoidal sigma weight residual 300.00 179.79 120.21 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 6729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 768 0.081 - 0.163: 641 0.163 - 0.244: 252 0.244 - 0.325: 42 0.325 - 0.406: 3 Chirality restraints: 1706 Sorted by residual: chirality pdb=" CA TYR B 528 " pdb=" N TYR B 528 " pdb=" C TYR B 528 " pdb=" CB TYR B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA TYR B 635 " pdb=" N TYR B 635 " pdb=" C TYR B 635 " pdb=" CB TYR B 635 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA TYR A 635 " pdb=" N TYR A 635 " pdb=" C TYR A 635 " pdb=" CB TYR A 635 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 1703 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 275 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ARG B 275 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG B 275 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 276 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 642 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA B 642 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA B 642 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 643 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 378 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C LEU A 378 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A 378 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 379 " -0.018 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 4439 2.95 - 3.44: 11252 3.44 - 3.93: 18417 3.93 - 4.41: 20923 4.41 - 4.90: 33105 Nonbonded interactions: 88136 Sorted by model distance: nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.465 2.496 nonbonded pdb=" N VAL B 781 " pdb=" O VAL B 781 " model vdw 2.473 2.496 nonbonded pdb=" N VAL A 781 " pdb=" O VAL A 781 " model vdw 2.486 2.496 nonbonded pdb=" N ASP B 139 " pdb=" O ASP B 139 " model vdw 2.489 2.496 nonbonded pdb=" N THR A 56 " pdb=" O THR A 56 " model vdw 2.510 2.496 ... (remaining 88131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 56 or resid 67 through 94 or resid 109 through \ 412 or resid 520 through 800 or resid 1801)) selection = (chain 'B' and (resid 17 through 662 or resid 667 through 800 or resid 1801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.120 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.010 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.112 10976 Z= 0.865 Angle : 1.801 12.564 14869 Z= 1.382 Chirality : 0.120 0.406 1706 Planarity : 0.008 0.034 1934 Dihedral : 14.072 133.634 4156 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Cbeta Deviations : 0.31 % 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: 1.53 (0.21), residues: 1355 helix: 2.66 (0.18), residues: 649 sheet: -0.52 (0.37), residues: 148 loop : -0.55 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 137 HIS 0.007 0.002 HIS B 312 PHE 0.021 0.004 PHE A 730 TYR 0.037 0.005 TYR B 528 ARG 0.025 0.002 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9234 (m) cc_final: 0.8768 (p) REVERT: A 260 MET cc_start: 0.6887 (tpt) cc_final: 0.6471 (tpp) REVERT: A 323 GLU cc_start: 0.8661 (tt0) cc_final: 0.8196 (tm-30) REVERT: A 365 LEU cc_start: 0.8581 (mt) cc_final: 0.7161 (mt) REVERT: A 441 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (p0) REVERT: A 528 TYR cc_start: 0.6743 (t80) cc_final: 0.6098 (t80) REVERT: A 552 LEU cc_start: 0.9147 (tp) cc_final: 0.8843 (mp) REVERT: A 615 PRO cc_start: 0.6031 (Cg_endo) cc_final: 0.3607 (Cg_exo) REVERT: A 617 MET cc_start: 0.8204 (mmm) cc_final: 0.7295 (mmt) REVERT: A 740 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8134 (pm20) REVERT: B 73 TYR cc_start: 0.5483 (p90) cc_final: 0.5127 (p90) REVERT: B 157 LEU cc_start: 0.7350 (tp) cc_final: 0.6803 (pp) REVERT: B 158 SER cc_start: 0.5808 (p) cc_final: 0.5407 (t) REVERT: B 173 THR cc_start: 0.7410 (p) cc_final: 0.6974 (t) REVERT: B 333 ASP cc_start: 0.8353 (m-30) cc_final: 0.7833 (t0) REVERT: B 368 MET cc_start: 0.7736 (ttm) cc_final: 0.7527 (ttm) REVERT: B 524 GLU cc_start: 0.7075 (pt0) cc_final: 0.6849 (mm-30) REVERT: B 602 ASN cc_start: 0.7724 (m-40) cc_final: 0.7449 (m-40) REVERT: B 687 TYR cc_start: 0.7565 (m-80) cc_final: 0.7021 (m-80) REVERT: B 718 LYS cc_start: 0.7581 (mttp) cc_final: 0.7194 (tmtt) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.3271 time to fit residues: 152.9521 Evaluate side-chains 236 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN B 760 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10976 Z= 0.303 Angle : 0.754 9.067 14869 Z= 0.387 Chirality : 0.045 0.198 1706 Planarity : 0.006 0.076 1934 Dihedral : 7.486 122.802 1532 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.35 % Allowed : 3.35 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1355 helix: 1.41 (0.19), residues: 658 sheet: -0.42 (0.34), residues: 165 loop : -0.62 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 709 HIS 0.014 0.002 HIS B 370 PHE 0.026 0.002 PHE B 155 TYR 0.034 0.003 TYR B 528 ARG 0.010 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 271 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7823 (tp) cc_final: 0.7066 (tp) REVERT: A 157 LEU cc_start: 0.8141 (tt) cc_final: 0.7926 (tt) REVERT: A 206 ILE cc_start: 0.8976 (mp) cc_final: 0.8703 (tt) REVERT: A 260 MET cc_start: 0.6737 (tpt) cc_final: 0.6524 (tpp) REVERT: A 323 GLU cc_start: 0.8379 (tt0) cc_final: 0.8147 (tm-30) REVERT: A 365 LEU cc_start: 0.8596 (mt) cc_final: 0.7591 (mt) REVERT: A 382 LEU cc_start: 0.8498 (mt) cc_final: 0.8063 (mt) REVERT: A 397 MET cc_start: 0.8693 (mtm) cc_final: 0.8201 (mtt) REVERT: A 441 ASP cc_start: 0.8683 (m-30) cc_final: 0.8288 (p0) REVERT: A 528 TYR cc_start: 0.6690 (t80) cc_final: 0.6484 (t80) REVERT: A 531 LEU cc_start: 0.9099 (mm) cc_final: 0.8899 (tp) REVERT: A 552 LEU cc_start: 0.9212 (tp) cc_final: 0.8984 (mt) REVERT: A 582 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7996 (mp0) REVERT: A 615 PRO cc_start: 0.6566 (Cg_endo) cc_final: 0.4862 (Cg_exo) REVERT: A 617 MET cc_start: 0.7608 (mmm) cc_final: 0.7407 (mmt) REVERT: B 20 LEU cc_start: 0.8968 (tp) cc_final: 0.8660 (tp) REVERT: B 49 GLN cc_start: 0.4574 (OUTLIER) cc_final: 0.4333 (pm20) REVERT: B 526 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: B 529 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8169 (tm-30) REVERT: B 533 ASP cc_start: 0.7388 (m-30) cc_final: 0.7149 (m-30) REVERT: B 617 MET cc_start: 0.7203 (mmt) cc_final: 0.6624 (mmp) REVERT: B 644 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7335 (ptmm) REVERT: B 692 MET cc_start: 0.5880 (ttm) cc_final: 0.4915 (ttm) REVERT: B 718 LYS cc_start: 0.7505 (mttp) cc_final: 0.7241 (tmtt) REVERT: B 724 LEU cc_start: 0.8282 (mt) cc_final: 0.8079 (mt) outliers start: 4 outliers final: 0 residues processed: 275 average time/residue: 0.3184 time to fit residues: 115.1394 Evaluate side-chains 194 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10976 Z= 0.248 Angle : 0.704 7.648 14869 Z= 0.357 Chirality : 0.043 0.174 1706 Planarity : 0.005 0.060 1934 Dihedral : 7.267 118.932 1532 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1355 helix: 1.05 (0.19), residues: 651 sheet: -0.40 (0.35), residues: 181 loop : -0.70 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 709 HIS 0.007 0.001 HIS B 370 PHE 0.019 0.002 PHE B 334 TYR 0.034 0.002 TYR B 31 ARG 0.010 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7031 (mtm) cc_final: 0.6743 (mtt) REVERT: A 40 PHE cc_start: 0.6404 (m-10) cc_final: 0.6148 (m-80) REVERT: A 83 LEU cc_start: 0.7765 (mt) cc_final: 0.7457 (mt) REVERT: A 143 PHE cc_start: 0.6291 (m-80) cc_final: 0.6039 (m-80) REVERT: A 170 LEU cc_start: 0.8043 (mt) cc_final: 0.7811 (mt) REVERT: A 172 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.4851 (tpp-160) REVERT: A 206 ILE cc_start: 0.9016 (mp) cc_final: 0.8765 (tp) REVERT: A 229 ASN cc_start: 0.8949 (t0) cc_final: 0.8700 (t0) REVERT: A 260 MET cc_start: 0.6816 (tpt) cc_final: 0.6601 (tpp) REVERT: A 269 MET cc_start: 0.5822 (ptm) cc_final: 0.5576 (ptp) REVERT: A 308 LYS cc_start: 0.6867 (ttmt) cc_final: 0.6661 (ttpt) REVERT: A 323 GLU cc_start: 0.8413 (tt0) cc_final: 0.8203 (tm-30) REVERT: A 397 MET cc_start: 0.8708 (mtm) cc_final: 0.8230 (mtt) REVERT: A 441 ASP cc_start: 0.8639 (m-30) cc_final: 0.8379 (p0) REVERT: A 552 LEU cc_start: 0.9234 (tp) cc_final: 0.8998 (mt) REVERT: A 582 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7959 (mp0) REVERT: A 615 PRO cc_start: 0.6761 (Cg_endo) cc_final: 0.5590 (Cg_exo) REVERT: A 617 MET cc_start: 0.8071 (mmm) cc_final: 0.7717 (mmm) REVERT: A 673 GLU cc_start: 0.7766 (pt0) cc_final: 0.7038 (pt0) REVERT: B 157 LEU cc_start: 0.7745 (tp) cc_final: 0.7492 (tp) REVERT: B 269 MET cc_start: 0.8346 (ttp) cc_final: 0.8054 (ttm) REVERT: B 365 LEU cc_start: 0.6652 (mt) cc_final: 0.6248 (mt) REVERT: B 524 GLU cc_start: 0.7787 (pt0) cc_final: 0.6151 (mm-30) REVERT: B 529 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7986 (tm-30) REVERT: B 533 ASP cc_start: 0.7271 (m-30) cc_final: 0.7013 (m-30) REVERT: B 705 LEU cc_start: 0.7548 (tp) cc_final: 0.7182 (tp) REVERT: B 718 LYS cc_start: 0.7596 (mttp) cc_final: 0.7352 (tmtt) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.2846 time to fit residues: 93.8971 Evaluate side-chains 188 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 0.0670 chunk 132 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 35 optimal weight: 0.0470 overall best weight: 1.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 538 HIS A 557 ASN A 643 GLN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10976 Z= 0.192 Angle : 0.672 8.892 14869 Z= 0.337 Chirality : 0.043 0.173 1706 Planarity : 0.005 0.042 1934 Dihedral : 6.867 114.575 1532 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1355 helix: 1.19 (0.20), residues: 654 sheet: -0.33 (0.36), residues: 171 loop : -0.74 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.005 0.001 HIS A 312 PHE 0.021 0.002 PHE A 155 TYR 0.024 0.002 TYR B 31 ARG 0.005 0.001 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6915 (mtm) cc_final: 0.6607 (mtt) REVERT: A 40 PHE cc_start: 0.5836 (m-10) cc_final: 0.5552 (m-80) REVERT: A 143 PHE cc_start: 0.6201 (m-80) cc_final: 0.5846 (m-80) REVERT: A 157 LEU cc_start: 0.8472 (mm) cc_final: 0.8188 (mm) REVERT: A 206 ILE cc_start: 0.8979 (mp) cc_final: 0.8591 (tp) REVERT: A 229 ASN cc_start: 0.8889 (t0) cc_final: 0.8579 (t0) REVERT: A 260 MET cc_start: 0.6716 (tpt) cc_final: 0.6510 (tpp) REVERT: A 269 MET cc_start: 0.5746 (ptm) cc_final: 0.5465 (ptp) REVERT: A 397 MET cc_start: 0.8638 (mtm) cc_final: 0.8206 (mtt) REVERT: A 441 ASP cc_start: 0.8739 (m-30) cc_final: 0.8353 (p0) REVERT: A 552 LEU cc_start: 0.9232 (tp) cc_final: 0.8985 (mt) REVERT: A 582 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7903 (mp0) REVERT: A 602 ASN cc_start: 0.8675 (m-40) cc_final: 0.8322 (m-40) REVERT: A 615 PRO cc_start: 0.6712 (Cg_endo) cc_final: 0.5522 (Cg_exo) REVERT: A 617 MET cc_start: 0.8111 (mmm) cc_final: 0.7747 (mmm) REVERT: B 269 MET cc_start: 0.8507 (ttp) cc_final: 0.8197 (ttm) REVERT: B 524 GLU cc_start: 0.7666 (pt0) cc_final: 0.6055 (mm-30) REVERT: B 529 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7975 (tm-30) REVERT: B 533 ASP cc_start: 0.7240 (m-30) cc_final: 0.6974 (m-30) REVERT: B 573 ILE cc_start: 0.7791 (pt) cc_final: 0.7516 (mp) REVERT: B 644 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8188 (tptt) REVERT: B 654 PHE cc_start: 0.4368 (m-80) cc_final: 0.4019 (m-80) REVERT: B 705 LEU cc_start: 0.7628 (tp) cc_final: 0.7339 (tp) REVERT: B 718 LYS cc_start: 0.7711 (mttp) cc_final: 0.7403 (tmtt) REVERT: B 725 PHE cc_start: 0.4841 (m-80) cc_final: 0.4487 (m-80) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.2427 time to fit residues: 73.7791 Evaluate side-chains 178 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 91 optimal weight: 0.3980 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 557 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 242 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10976 Z= 0.257 Angle : 0.709 8.347 14869 Z= 0.353 Chirality : 0.043 0.220 1706 Planarity : 0.005 0.070 1934 Dihedral : 6.719 111.380 1532 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1355 helix: 1.04 (0.20), residues: 648 sheet: -0.27 (0.36), residues: 166 loop : -0.86 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 709 HIS 0.006 0.001 HIS B 585 PHE 0.014 0.002 PHE A 532 TYR 0.023 0.002 TYR A 635 ARG 0.014 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7047 (mtm) cc_final: 0.6638 (mtt) REVERT: A 40 PHE cc_start: 0.6222 (m-10) cc_final: 0.5936 (m-80) REVERT: A 113 ILE cc_start: 0.8020 (mp) cc_final: 0.7797 (mp) REVERT: A 143 PHE cc_start: 0.6402 (m-80) cc_final: 0.6118 (m-80) REVERT: A 157 LEU cc_start: 0.8532 (mm) cc_final: 0.8308 (mm) REVERT: A 170 LEU cc_start: 0.8033 (mt) cc_final: 0.7726 (mt) REVERT: A 184 PHE cc_start: 0.4633 (t80) cc_final: 0.4305 (t80) REVERT: A 229 ASN cc_start: 0.8908 (t0) cc_final: 0.8528 (t0) REVERT: A 260 MET cc_start: 0.6650 (tpt) cc_final: 0.6424 (tpp) REVERT: A 397 MET cc_start: 0.8656 (mtm) cc_final: 0.8074 (mtt) REVERT: A 441 ASP cc_start: 0.8815 (m-30) cc_final: 0.8418 (p0) REVERT: A 552 LEU cc_start: 0.9235 (tp) cc_final: 0.9019 (mt) REVERT: A 582 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7860 (mp0) REVERT: A 615 PRO cc_start: 0.6934 (Cg_endo) cc_final: 0.5827 (Cg_exo) REVERT: A 617 MET cc_start: 0.8191 (mmm) cc_final: 0.7906 (mmm) REVERT: B 269 MET cc_start: 0.8407 (ttp) cc_final: 0.8097 (ttm) REVERT: B 386 ASP cc_start: 0.7869 (p0) cc_final: 0.7650 (p0) REVERT: B 524 GLU cc_start: 0.7791 (pt0) cc_final: 0.6071 (mm-30) REVERT: B 529 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8064 (tm-30) REVERT: B 533 ASP cc_start: 0.7177 (m-30) cc_final: 0.6808 (m-30) REVERT: B 573 ILE cc_start: 0.7858 (pt) cc_final: 0.7631 (mp) REVERT: B 624 MET cc_start: 0.8341 (tmm) cc_final: 0.8116 (ttp) REVERT: B 705 LEU cc_start: 0.7607 (tp) cc_final: 0.7322 (tp) REVERT: B 717 ASN cc_start: 0.7929 (t0) cc_final: 0.7581 (t0) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2800 time to fit residues: 79.7370 Evaluate side-chains 158 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10976 Z= 0.310 Angle : 0.770 7.391 14869 Z= 0.391 Chirality : 0.045 0.186 1706 Planarity : 0.005 0.054 1934 Dihedral : 6.908 110.638 1532 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1355 helix: 0.63 (0.20), residues: 652 sheet: -0.41 (0.37), residues: 170 loop : -0.94 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 137 HIS 0.007 0.001 HIS B 585 PHE 0.024 0.002 PHE B 670 TYR 0.025 0.003 TYR A 635 ARG 0.013 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6790 (m-10) cc_final: 0.6570 (m-80) REVERT: A 143 PHE cc_start: 0.6637 (m-80) cc_final: 0.6056 (m-10) REVERT: A 157 LEU cc_start: 0.8785 (mm) cc_final: 0.8005 (tp) REVERT: A 184 PHE cc_start: 0.4754 (t80) cc_final: 0.4474 (t80) REVERT: A 229 ASN cc_start: 0.8973 (t0) cc_final: 0.8465 (t0) REVERT: A 397 MET cc_start: 0.8541 (mtm) cc_final: 0.7954 (mtt) REVERT: A 441 ASP cc_start: 0.8889 (m-30) cc_final: 0.8481 (p0) REVERT: A 552 LEU cc_start: 0.9249 (tp) cc_final: 0.9020 (mt) REVERT: A 582 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7887 (mp0) REVERT: A 615 PRO cc_start: 0.7194 (Cg_endo) cc_final: 0.6158 (Cg_exo) REVERT: A 617 MET cc_start: 0.8270 (mmm) cc_final: 0.7871 (mmt) REVERT: A 626 GLN cc_start: 0.7879 (tt0) cc_final: 0.7607 (tt0) REVERT: A 739 MET cc_start: 0.8396 (ptm) cc_final: 0.8021 (tmm) REVERT: B 73 TYR cc_start: 0.6267 (p90) cc_final: 0.5883 (p90) REVERT: B 269 MET cc_start: 0.8448 (ttp) cc_final: 0.8064 (ttt) REVERT: B 386 ASP cc_start: 0.7908 (p0) cc_final: 0.7652 (p0) REVERT: B 529 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8231 (tm-30) REVERT: B 533 ASP cc_start: 0.7229 (m-30) cc_final: 0.6823 (m-30) REVERT: B 717 ASN cc_start: 0.8251 (t0) cc_final: 0.7783 (t0) REVERT: B 725 PHE cc_start: 0.5349 (m-80) cc_final: 0.4100 (m-10) REVERT: B 752 HIS cc_start: 0.8242 (p-80) cc_final: 0.7956 (p-80) REVERT: B 795 GLU cc_start: 0.8230 (pp20) cc_final: 0.7916 (pp20) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2254 time to fit residues: 64.1690 Evaluate side-chains 158 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 overall best weight: 2.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10976 Z= 0.206 Angle : 0.692 7.440 14869 Z= 0.346 Chirality : 0.043 0.306 1706 Planarity : 0.005 0.072 1934 Dihedral : 6.506 107.920 1532 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1355 helix: 0.99 (0.20), residues: 649 sheet: -0.04 (0.38), residues: 162 loop : -0.97 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 137 HIS 0.007 0.001 HIS B 585 PHE 0.013 0.002 PHE A 532 TYR 0.034 0.002 TYR B 31 ARG 0.015 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6359 (m-10) cc_final: 0.6106 (m-80) REVERT: A 143 PHE cc_start: 0.6331 (m-80) cc_final: 0.5839 (m-10) REVERT: A 184 PHE cc_start: 0.4695 (t80) cc_final: 0.4452 (t80) REVERT: A 229 ASN cc_start: 0.8930 (t0) cc_final: 0.8456 (t0) REVERT: A 321 LEU cc_start: 0.8952 (mm) cc_final: 0.8711 (mt) REVERT: A 397 MET cc_start: 0.8510 (mtm) cc_final: 0.8014 (mtt) REVERT: A 432 GLU cc_start: 0.8488 (tt0) cc_final: 0.7562 (tp30) REVERT: A 441 ASP cc_start: 0.8774 (m-30) cc_final: 0.8330 (p0) REVERT: A 552 LEU cc_start: 0.9213 (tp) cc_final: 0.8877 (mp) REVERT: A 582 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7894 (mp0) REVERT: A 615 PRO cc_start: 0.6856 (Cg_endo) cc_final: 0.5765 (Cg_exo) REVERT: A 617 MET cc_start: 0.8216 (mmm) cc_final: 0.7906 (mmt) REVERT: A 739 MET cc_start: 0.8206 (ptm) cc_final: 0.7872 (tmm) REVERT: B 73 TYR cc_start: 0.6192 (p90) cc_final: 0.5814 (p90) REVERT: B 187 MET cc_start: 0.4686 (mmm) cc_final: 0.4346 (mmm) REVERT: B 189 LEU cc_start: 0.8438 (mm) cc_final: 0.8196 (mp) REVERT: B 386 ASP cc_start: 0.7819 (p0) cc_final: 0.7582 (p0) REVERT: B 524 GLU cc_start: 0.7643 (pt0) cc_final: 0.6063 (mm-30) REVERT: B 529 GLU cc_start: 0.8808 (mm-30) cc_final: 0.7991 (tm-30) REVERT: B 533 ASP cc_start: 0.7186 (m-30) cc_final: 0.6837 (m-30) REVERT: B 624 MET cc_start: 0.7557 (mtp) cc_final: 0.7030 (mtp) REVERT: B 717 ASN cc_start: 0.8016 (t0) cc_final: 0.7454 (t0) REVERT: B 725 PHE cc_start: 0.6234 (m-80) cc_final: 0.6033 (m-80) REVERT: B 750 LEU cc_start: 0.8422 (tp) cc_final: 0.8087 (tp) REVERT: B 759 MET cc_start: 0.8448 (mmp) cc_final: 0.8203 (mmp) REVERT: B 795 GLU cc_start: 0.8276 (pp20) cc_final: 0.7983 (pp20) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2328 time to fit residues: 65.7630 Evaluate side-chains 154 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10976 Z= 0.275 Angle : 0.738 8.582 14869 Z= 0.370 Chirality : 0.044 0.172 1706 Planarity : 0.005 0.041 1934 Dihedral : 6.554 104.525 1532 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1355 helix: 0.86 (0.20), residues: 646 sheet: -0.18 (0.38), residues: 169 loop : -1.09 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 137 HIS 0.016 0.001 HIS B 370 PHE 0.021 0.002 PHE A 30 TYR 0.029 0.003 TYR B 31 ARG 0.008 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6644 (m-80) cc_final: 0.6114 (m-10) REVERT: A 166 MET cc_start: 0.6515 (tpt) cc_final: 0.6241 (tpp) REVERT: A 184 PHE cc_start: 0.4631 (t80) cc_final: 0.4413 (t80) REVERT: A 229 ASN cc_start: 0.8965 (t0) cc_final: 0.8519 (t0) REVERT: A 397 MET cc_start: 0.8453 (mtm) cc_final: 0.7951 (mtt) REVERT: A 441 ASP cc_start: 0.8837 (m-30) cc_final: 0.8359 (p0) REVERT: A 552 LEU cc_start: 0.9264 (tp) cc_final: 0.8905 (mp) REVERT: A 582 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7952 (mp0) REVERT: A 615 PRO cc_start: 0.7316 (Cg_endo) cc_final: 0.6138 (Cg_exo) REVERT: A 617 MET cc_start: 0.8283 (mmm) cc_final: 0.7991 (mmt) REVERT: A 739 MET cc_start: 0.8270 (ptm) cc_final: 0.7999 (tmm) REVERT: B 73 TYR cc_start: 0.6473 (p90) cc_final: 0.5953 (p90) REVERT: B 187 MET cc_start: 0.4660 (mmm) cc_final: 0.4270 (mmm) REVERT: B 351 ILE cc_start: 0.2282 (mm) cc_final: 0.1074 (mm) REVERT: B 368 MET cc_start: 0.7508 (ptp) cc_final: 0.7259 (ptp) REVERT: B 386 ASP cc_start: 0.7877 (p0) cc_final: 0.7562 (p0) REVERT: B 529 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8154 (tm-30) REVERT: B 533 ASP cc_start: 0.7291 (m-30) cc_final: 0.6895 (m-30) REVERT: B 691 LEU cc_start: 0.7762 (mt) cc_final: 0.7545 (mp) REVERT: B 692 MET cc_start: 0.3807 (ttt) cc_final: 0.3310 (ttt) REVERT: B 717 ASN cc_start: 0.8189 (t0) cc_final: 0.7597 (t0) REVERT: B 725 PHE cc_start: 0.5681 (m-80) cc_final: 0.4500 (m-10) REVERT: B 795 GLU cc_start: 0.8319 (pp20) cc_final: 0.8023 (pp20) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2307 time to fit residues: 63.7543 Evaluate side-chains 151 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 50.0000 chunk 126 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN B 752 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10976 Z= 0.233 Angle : 0.726 11.498 14869 Z= 0.360 Chirality : 0.043 0.173 1706 Planarity : 0.005 0.046 1934 Dihedral : 6.416 103.207 1532 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1355 helix: 0.96 (0.20), residues: 645 sheet: -0.10 (0.40), residues: 152 loop : -1.15 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 137 HIS 0.013 0.001 HIS B 370 PHE 0.015 0.002 PHE A 758 TYR 0.029 0.002 TYR B 31 ARG 0.006 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6725 (m-80) cc_final: 0.6219 (m-10) REVERT: A 184 PHE cc_start: 0.4945 (t80) cc_final: 0.4645 (t80) REVERT: A 229 ASN cc_start: 0.8966 (t0) cc_final: 0.8507 (t0) REVERT: A 382 LEU cc_start: 0.8316 (mt) cc_final: 0.7948 (tp) REVERT: A 397 MET cc_start: 0.8398 (mtm) cc_final: 0.8022 (mtt) REVERT: A 441 ASP cc_start: 0.8819 (m-30) cc_final: 0.8307 (p0) REVERT: A 552 LEU cc_start: 0.9262 (tp) cc_final: 0.8982 (mt) REVERT: A 582 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8049 (mp0) REVERT: A 615 PRO cc_start: 0.7212 (Cg_endo) cc_final: 0.6070 (Cg_exo) REVERT: A 617 MET cc_start: 0.8322 (mmm) cc_final: 0.7992 (mmm) REVERT: A 739 MET cc_start: 0.8201 (ptm) cc_final: 0.7979 (tmm) REVERT: A 750 LEU cc_start: 0.8853 (pt) cc_final: 0.8616 (pt) REVERT: B 73 TYR cc_start: 0.6532 (p90) cc_final: 0.6125 (p90) REVERT: B 187 MET cc_start: 0.4422 (mmm) cc_final: 0.4086 (mmm) REVERT: B 189 LEU cc_start: 0.8475 (mm) cc_final: 0.8223 (mp) REVERT: B 288 GLU cc_start: 0.8667 (mp0) cc_final: 0.8386 (mp0) REVERT: B 351 ILE cc_start: 0.2328 (mm) cc_final: 0.1116 (mm) REVERT: B 368 MET cc_start: 0.7110 (ptp) cc_final: 0.6798 (ptp) REVERT: B 386 ASP cc_start: 0.7862 (p0) cc_final: 0.7518 (p0) REVERT: B 529 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8058 (tm-30) REVERT: B 533 ASP cc_start: 0.7334 (m-30) cc_final: 0.6962 (m-30) REVERT: B 691 LEU cc_start: 0.7752 (mt) cc_final: 0.7488 (mp) REVERT: B 795 GLU cc_start: 0.8374 (pp20) cc_final: 0.8104 (pp20) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2422 time to fit residues: 63.0461 Evaluate side-chains 149 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 391 GLN A 557 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 326 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN B 734 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10976 Z= 0.284 Angle : 0.754 9.740 14869 Z= 0.379 Chirality : 0.044 0.179 1706 Planarity : 0.005 0.042 1934 Dihedral : 6.507 102.358 1532 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1355 helix: 0.83 (0.20), residues: 643 sheet: -0.21 (0.40), residues: 151 loop : -1.28 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 137 HIS 0.010 0.001 HIS B 370 PHE 0.015 0.002 PHE B 184 TYR 0.023 0.003 TYR B 31 ARG 0.009 0.001 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6991 (m-80) cc_final: 0.6548 (m-10) REVERT: A 184 PHE cc_start: 0.4666 (t80) cc_final: 0.4398 (t80) REVERT: A 229 ASN cc_start: 0.8989 (t0) cc_final: 0.8525 (t0) REVERT: A 382 LEU cc_start: 0.8261 (mt) cc_final: 0.7939 (tp) REVERT: A 397 MET cc_start: 0.8447 (mtm) cc_final: 0.8052 (mtt) REVERT: A 441 ASP cc_start: 0.8880 (m-30) cc_final: 0.8362 (p0) REVERT: A 552 LEU cc_start: 0.9283 (tp) cc_final: 0.8924 (mp) REVERT: A 582 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8182 (mp0) REVERT: A 615 PRO cc_start: 0.7361 (Cg_endo) cc_final: 0.6310 (Cg_exo) REVERT: A 626 GLN cc_start: 0.7981 (tt0) cc_final: 0.7660 (tt0) REVERT: A 739 MET cc_start: 0.8297 (ptm) cc_final: 0.8051 (tmm) REVERT: A 750 LEU cc_start: 0.8855 (pt) cc_final: 0.8539 (pt) REVERT: A 784 GLU cc_start: 0.8504 (pm20) cc_final: 0.8279 (pm20) REVERT: B 73 TYR cc_start: 0.6714 (p90) cc_final: 0.6272 (p90) REVERT: B 187 MET cc_start: 0.4739 (mmm) cc_final: 0.4412 (mmm) REVERT: B 189 LEU cc_start: 0.8535 (mm) cc_final: 0.8291 (mp) REVERT: B 269 MET cc_start: 0.8467 (ttp) cc_final: 0.8177 (ttm) REVERT: B 351 ILE cc_start: 0.2493 (mm) cc_final: 0.1358 (mm) REVERT: B 368 MET cc_start: 0.7110 (ptp) cc_final: 0.6852 (ptp) REVERT: B 386 ASP cc_start: 0.7718 (p0) cc_final: 0.7328 (p0) REVERT: B 739 MET cc_start: 0.6781 (tmm) cc_final: 0.6581 (tmm) REVERT: B 750 LEU cc_start: 0.8257 (tp) cc_final: 0.7652 (tp) REVERT: B 759 MET cc_start: 0.8434 (mmp) cc_final: 0.8075 (mmp) REVERT: B 778 LEU cc_start: 0.8377 (pp) cc_final: 0.8088 (pp) REVERT: B 795 GLU cc_start: 0.8261 (pp20) cc_final: 0.7925 (pp20) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.2500 time to fit residues: 64.8070 Evaluate side-chains 154 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 216 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.067429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059313 restraints weight = 72070.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.060692 restraints weight = 52016.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.061735 restraints weight = 39158.506| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.8318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10976 Z= 0.293 Angle : 0.773 9.502 14869 Z= 0.388 Chirality : 0.045 0.179 1706 Planarity : 0.005 0.046 1934 Dihedral : 6.598 101.183 1532 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 30.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % 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: -0.40 (0.22), residues: 1355 helix: 0.68 (0.20), residues: 642 sheet: -0.27 (0.39), residues: 160 loop : -1.36 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 137 HIS 0.010 0.001 HIS B 370 PHE 0.015 0.002 PHE B 184 TYR 0.023 0.003 TYR A 635 ARG 0.010 0.001 ARG B 319 =============================================================================== Job complete usr+sys time: 2252.71 seconds wall clock time: 47 minutes 30.98 seconds (2850.98 seconds total)