Starting phenix.real_space_refine (version: dev) on Sun Feb 19 22:16:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2023/7ou2_13073_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2023/7ou2_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_2023/7ou2_13073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2023/7ou2_13073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2023/7ou2_13073_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou2_13073/02_2023/7ou2_13073_neut_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 7.28, per 1000 atoms: 0.67 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: 4.63 Conformation dependent library (CDL) restraints added in 1.6 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: 1.42 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: 3.85 Time building geometry restraints manager: 5.00 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 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. 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: 0.090 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: 1.540 Check model and map are aligned: 0.140 Process input model: 32.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 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 % 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 *********************** 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 : 1.292 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 outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.3292 time to fit residues: 153.8447 Evaluate side-chains 229 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8607 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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 760 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 10976 Z= 0.296 Angle : 0.758 9.536 14869 Z= 0.389 Chirality : 0.045 0.176 1706 Planarity : 0.006 0.059 1934 Dihedral : 7.522 123.727 1532 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1355 helix: 1.39 (0.19), residues: 653 sheet: -0.46 (0.34), residues: 165 loop : -0.64 (0.24), residues: 537 *********************** 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 272 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 1.261 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 outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.3461 time to fit residues: 124.2130 Evaluate side-chains 189 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1454 time to fit residues: 2.0707 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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 ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN ** 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 49 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5206 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= 0.287 Angle : 0.729 10.092 14869 Z= 0.372 Chirality : 0.043 0.165 1706 Planarity : 0.005 0.053 1934 Dihedral : 7.351 119.386 1532 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.18 % 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: 0.12 (0.21), residues: 1355 helix: 0.95 (0.19), residues: 661 sheet: -0.51 (0.34), residues: 187 loop : -0.73 (0.24), residues: 507 *********************** 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 246 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.300 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 outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.2933 time to fit residues: 96.6489 Evaluate side-chains 180 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1388 time to fit residues: 1.9101 ------------------------------------------------------------------------------- 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: 20.0000 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 0.0070 chunk 132 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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 381 GLN ** 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 391 GLN 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: 0.6779 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10976 Z= 0.201 Angle : 0.674 8.094 14869 Z= 0.340 Chirality : 0.042 0.174 1706 Planarity : 0.005 0.055 1934 Dihedral : 6.962 115.226 1532 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.09 % 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: 0.26 (0.22), residues: 1355 helix: 1.13 (0.20), residues: 658 sheet: -0.48 (0.35), residues: 177 loop : -0.74 (0.25), residues: 520 *********************** 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 222 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.302 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 outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.2848 time to fit residues: 85.4425 Evaluate side-chains 173 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1359 time to fit residues: 2.0161 ------------------------------------------------------------------------------- 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: 20.0000 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.0270 chunk 118 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 3.3244 ------------------------------------------------------------------------------- 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 538 HIS A 557 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 242 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10976 Z= 0.204 Angle : 0.678 9.188 14869 Z= 0.337 Chirality : 0.041 0.172 1706 Planarity : 0.005 0.077 1934 Dihedral : 6.681 111.570 1532 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1355 helix: 1.23 (0.20), residues: 647 sheet: -0.54 (0.35), residues: 175 loop : -0.78 (0.24), residues: 533 *********************** 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: 3 poor density : 209 time to evaluate : 1.257 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 outliers start: 3 outliers final: 1 residues processed: 212 average time/residue: 0.2920 time to fit residues: 83.8314 Evaluate side-chains 167 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2149 time to fit residues: 2.3488 ------------------------------------------------------------------------------- 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: 8.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 381 GLN A 557 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 557 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10976 Z= 0.206 Angle : 0.687 9.058 14869 Z= 0.343 Chirality : 0.042 0.202 1706 Planarity : 0.005 0.053 1934 Dihedral : 6.521 109.317 1532 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.09 % 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: 1.14 (0.20), residues: 648 sheet: -0.41 (0.36), residues: 186 loop : -0.79 (0.24), residues: 521 *********************** 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 209 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.379 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 outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2738 time to fit residues: 78.2473 Evaluate side-chains 163 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7412 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 0.0470 chunk 82 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- 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 229 ASN ** 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 626 GLN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** 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 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6894 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10976 Z= 0.238 Angle : 0.712 8.302 14869 Z= 0.361 Chirality : 0.043 0.198 1706 Planarity : 0.005 0.056 1934 Dihedral : 6.527 106.630 1532 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.18 % 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: 0.14 (0.22), residues: 1355 helix: 1.15 (0.20), residues: 647 sheet: -0.37 (0.39), residues: 164 loop : -1.00 (0.24), residues: 544 *********************** 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 205 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 1.483 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 outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2749 time to fit residues: 77.0277 Evaluate side-chains 159 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6292 ------------------------------------------------------------------------------- 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: 30.0000 chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 557 ASN ** A 616 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 126 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** 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: 0.6927 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10976 Z= 0.245 Angle : 0.728 7.309 14869 Z= 0.365 Chirality : 0.043 0.171 1706 Planarity : 0.006 0.134 1934 Dihedral : 6.522 104.320 1532 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.09 % 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: 1.08 (0.20), residues: 638 sheet: -0.53 (0.37), residues: 179 loop : -0.92 (0.25), residues: 538 *********************** 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 201 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.268 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 outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2929 time to fit residues: 79.6642 Evaluate side-chains 155 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7428 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 381 GLN A 557 ASN ** A 616 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 734 GLN ** 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: 0.6958 moved from start: 0.7438 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= 0.262 Angle : 0.742 8.783 14869 Z= 0.374 Chirality : 0.044 0.177 1706 Planarity : 0.006 0.109 1934 Dihedral : 6.517 100.414 1532 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.00 % 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: 0.99 (0.20), residues: 640 sheet: -0.51 (0.37), residues: 191 loop : -1.04 (0.25), residues: 524 *********************** 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 193 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.297 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 outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2855 time to fit residues: 75.0226 Evaluate side-chains 150 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7909 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 616 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 212 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS ** 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: 0.6950 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10976 Z= 0.227 Angle : 0.724 8.336 14869 Z= 0.364 Chirality : 0.044 0.211 1706 Planarity : 0.005 0.087 1934 Dihedral : 6.342 97.278 1532 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.00 % 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: 1.06 (0.20), residues: 644 sheet: -0.51 (0.36), residues: 199 loop : -1.02 (0.26), residues: 512 ********************** 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 184 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.312 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 outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2902 time to fit residues: 72.5868 Evaluate side-chains 152 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8053 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 ** 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 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** 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 752 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.067722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.059775 restraints weight = 73422.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.061125 restraints weight = 52907.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062148 restraints weight = 39929.700| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.8091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10976 Z= 0.319 Angle : 0.806 9.795 14869 Z= 0.409 Chirality : 0.046 0.192 1706 Planarity : 0.006 0.086 1934 Dihedral : 6.644 95.028 1532 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.00 % 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: -0.34 (0.22), residues: 1355 helix: 0.73 (0.20), residues: 640 sheet: -0.60 (0.37), residues: 194 loop : -1.21 (0.25), residues: 521 =============================================================================== Job complete usr+sys time: 2262.18 seconds wall clock time: 42 minutes 34.66 seconds (2554.66 seconds total)