Starting phenix.real_space_refine on Mon Mar 11 07:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/03_2024/6npy_0476_updated.pdb" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 4823 2.51 5 N 1286 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 924": "OD1" <-> "OD2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7586 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6192 Classifications: {'peptide': 798} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 25, 'TRANS': 772} Chain breaks: 7 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 1367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1385 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 284 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 284 " occ=0.50 Time building chain proxies: 5.10, per 1000 atoms: 0.67 Number of scatterers: 7586 At special positions: 0 Unit cell: (115.08, 89.88, 100.8, 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 70 16.00 P 2 15.00 O 1405 8.00 N 1286 7.00 C 4823 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 40.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.904A pdb=" N GLU A 354 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS A 358 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 410 through 417 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.826A pdb=" N TYR A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 4.042A pdb=" N TRP A 465 " --> pdb=" O CYS A 461 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 544 through 553 Proline residue: A 552 - end of helix Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.706A pdb=" N ILE A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 618 through 633 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 729 through 735 removed outlier: 5.093A pdb=" N VAL A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 760 through 763 No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 782 through 793 removed outlier: 4.699A pdb=" N PHE A 786 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 842 through 851 removed outlier: 4.264A pdb=" N SER A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.754A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 955 through 965 Processing helix chain 'A' and resid 980 through 992 removed outlier: 3.686A pdb=" N VAL A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 4.062A pdb=" N ALA A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.886A pdb=" N PHE B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 4.202A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 285 through 299 removed outlier: 4.170A pdb=" N ASP B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.411A pdb=" N LEU A 344 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE A 222 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 346 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'A' and resid 800 through 802 removed outlier: 7.435A pdb=" N LYS A 829 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 857 " --> pdb=" O LEU A 830 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 971 through 974 removed outlier: 6.162A pdb=" N ASN A1000 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU A 974 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A1002 " --> pdb=" O LEU A 974 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 210 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2435 1.34 - 1.46: 1641 1.46 - 1.58: 3564 1.58 - 1.70: 3 1.70 - 1.82: 96 Bond restraints: 7739 Sorted by residual: bond pdb=" C MET A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.18e+01 bond pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.54e-02 4.22e+03 2.93e+00 bond pdb=" C LYS A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.82e+00 bond pdb=" CB TRP A 831 " pdb=" CG TRP A 831 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.54e+00 bond pdb=" CA LEU A 746 " pdb=" CB LEU A 746 " ideal model delta sigma weight residual 1.531 1.480 0.051 3.28e-02 9.30e+02 2.39e+00 ... (remaining 7734 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.64: 226 106.64 - 114.03: 4394 114.03 - 121.42: 3960 121.42 - 128.81: 1812 128.81 - 136.20: 71 Bond angle restraints: 10463 Sorted by residual: angle pdb=" N VAL A 860 " pdb=" CA VAL A 860 " pdb=" C VAL A 860 " ideal model delta sigma weight residual 111.77 105.80 5.97 1.04e+00 9.25e-01 3.30e+01 angle pdb=" C GLN A 432 " pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 122.46 129.31 -6.85 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N ILE A 475 " pdb=" CA ILE A 475 " pdb=" C ILE A 475 " ideal model delta sigma weight residual 113.71 109.13 4.58 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C VAL A 262 " pdb=" N SER A 263 " pdb=" CA SER A 263 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N LEU A 551 " pdb=" CA LEU A 551 " pdb=" C LEU A 551 " ideal model delta sigma weight residual 109.81 118.79 -8.98 2.21e+00 2.05e-01 1.65e+01 ... (remaining 10458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4019 17.56 - 35.13: 530 35.13 - 52.69: 93 52.69 - 70.25: 14 70.25 - 87.81: 15 Dihedral angle restraints: 4671 sinusoidal: 1853 harmonic: 2818 Sorted by residual: dihedral pdb=" CA VAL A 860 " pdb=" C VAL A 860 " pdb=" N GLY A 861 " pdb=" CA GLY A 861 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA CYS A 784 " pdb=" C CYS A 784 " pdb=" N CYS A 785 " pdb=" CA CYS A 785 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO A 363 " pdb=" C PRO A 363 " pdb=" N ARG A 364 " pdb=" CA ARG A 364 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 944 0.073 - 0.146: 202 0.146 - 0.218: 30 0.218 - 0.291: 4 0.291 - 0.364: 3 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CB ILE A 480 " pdb=" CA ILE A 480 " pdb=" CG1 ILE A 480 " pdb=" CG2 ILE A 480 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 860 " pdb=" CA VAL A 860 " pdb=" CG1 VAL A 860 " pdb=" CG2 VAL A 860 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1180 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " -0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 284 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 648 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 649 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 649 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 649 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.028 2.00e-02 2.50e+03 2.08e-02 7.57e+00 pdb=" CG PHE A 648 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " 0.002 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1659 2.77 - 3.31: 7362 3.31 - 3.84: 12770 3.84 - 4.37: 14291 4.37 - 4.90: 23159 Nonbonded interactions: 59241 Sorted by model distance: nonbonded pdb=" O MET B 295 " pdb=" OG1 THR B 299 " model vdw 2.244 2.440 nonbonded pdb=" O SER A1014 " pdb=" OG1 THR A1018 " model vdw 2.251 2.440 nonbonded pdb=" O PRO B 134 " pdb=" OG1 THR B 137 " model vdw 2.254 2.440 nonbonded pdb=" O LEU A 706 " pdb=" OG SER A 709 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 570 " pdb=" O GLU A 585 " model vdw 2.278 2.440 ... (remaining 59236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 3.290 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.006 0.061 7739 Z= 0.415 Angle : 1.160 10.488 10463 Z= 0.608 Chirality : 0.063 0.364 1183 Planarity : 0.007 0.094 1327 Dihedral : 16.443 87.813 2841 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.63 % Favored : 85.26 % Rotamer: Outliers : 0.84 % Allowed : 13.58 % Favored : 85.58 % 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: -4.90 (0.22), residues: 946 helix: -3.04 (0.17), residues: 402 sheet: -3.72 (0.52), residues: 74 loop : -3.36 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 241 HIS 0.011 0.002 HIS A 698 PHE 0.045 0.003 PHE A 648 TYR 0.029 0.003 TYR A 531 ARG 0.005 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.928 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: A 241 TRP cc_start: 0.6672 (t60) cc_final: 0.6468 (t60) REVERT: A 254 LEU cc_start: 0.8144 (mt) cc_final: 0.7501 (mt) REVERT: A 302 PHE cc_start: 0.7308 (t80) cc_final: 0.7015 (t80) REVERT: A 567 GLU cc_start: 0.8336 (pp20) cc_final: 0.7432 (pp20) REVERT: A 571 LEU cc_start: 0.7718 (mt) cc_final: 0.6619 (mt) REVERT: A 630 TYR cc_start: 0.8223 (m-80) cc_final: 0.7946 (m-80) REVERT: A 685 MET cc_start: 0.8512 (tpt) cc_final: 0.8226 (tpt) REVERT: A 701 MET cc_start: 0.5707 (mmt) cc_final: 0.5429 (mmm) REVERT: A 782 HIS cc_start: 0.7189 (t70) cc_final: 0.6344 (t-90) REVERT: B 162 ILE cc_start: 0.7270 (mp) cc_final: 0.6215 (mp) REVERT: B 163 LYS cc_start: 0.7561 (mmtm) cc_final: 0.6747 (pttp) outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.2564 time to fit residues: 55.5743 Evaluate side-chains 132 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 895 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 782 HIS A 909 ASN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7739 Z= 0.209 Angle : 0.782 8.808 10463 Z= 0.390 Chirality : 0.045 0.234 1183 Planarity : 0.005 0.080 1327 Dihedral : 7.958 47.587 1048 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 3.85 % Allowed : 19.59 % Favored : 76.56 % 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: -3.56 (0.25), residues: 946 helix: -1.62 (0.23), residues: 400 sheet: -3.39 (0.55), residues: 69 loop : -2.90 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 957 HIS 0.004 0.001 HIS B 125 PHE 0.017 0.002 PHE A 648 TYR 0.022 0.002 TYR A 570 ARG 0.009 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7720 (m90) cc_final: 0.7439 (m90) REVERT: A 685 MET cc_start: 0.8505 (tpt) cc_final: 0.8139 (tpt) REVERT: A 701 MET cc_start: 0.5607 (mmt) cc_final: 0.5335 (mmm) REVERT: A 782 HIS cc_start: 0.6840 (t-90) cc_final: 0.6211 (t-90) REVERT: A 811 PHE cc_start: 0.7374 (t80) cc_final: 0.7142 (t80) REVERT: B 152 MET cc_start: 0.8671 (mtp) cc_final: 0.8300 (ttt) REVERT: B 158 MET cc_start: 0.5581 (mpp) cc_final: 0.5362 (mmt) REVERT: B 162 ILE cc_start: 0.7079 (mp) cc_final: 0.6120 (mp) REVERT: B 163 LYS cc_start: 0.7502 (mmtm) cc_final: 0.6683 (pttt) REVERT: B 166 ASN cc_start: 0.8325 (t0) cc_final: 0.7892 (t0) REVERT: B 207 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6920 (mmm160) outliers start: 32 outliers final: 19 residues processed: 165 average time/residue: 0.2145 time to fit residues: 47.3026 Evaluate side-chains 148 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 86 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.165 Angle : 0.729 9.390 10463 Z= 0.360 Chirality : 0.044 0.243 1183 Planarity : 0.005 0.077 1327 Dihedral : 7.405 50.679 1048 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 3.49 % Allowed : 22.96 % Favored : 73.56 % 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: -2.99 (0.26), residues: 946 helix: -1.04 (0.25), residues: 403 sheet: -3.23 (0.49), residues: 81 loop : -2.64 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 957 HIS 0.004 0.001 HIS B 125 PHE 0.014 0.001 PHE A 640 TYR 0.017 0.001 TYR A 633 ARG 0.009 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7746 (m90) cc_final: 0.7491 (m90) REVERT: A 521 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6402 (ptt) REVERT: A 571 LEU cc_start: 0.7356 (mt) cc_final: 0.6698 (mt) REVERT: A 701 MET cc_start: 0.5501 (mmt) cc_final: 0.5202 (mmm) REVERT: A 782 HIS cc_start: 0.6803 (t-90) cc_final: 0.6217 (t-90) REVERT: B 162 ILE cc_start: 0.7007 (mp) cc_final: 0.6343 (mp) REVERT: B 163 LYS cc_start: 0.7355 (mmtm) cc_final: 0.7068 (mmtt) REVERT: B 213 TYR cc_start: 0.4071 (t80) cc_final: 0.3756 (t80) REVERT: B 244 TYR cc_start: 0.8379 (t80) cc_final: 0.8135 (t80) REVERT: B 295 MET cc_start: 0.7542 (mmp) cc_final: 0.7338 (mmp) outliers start: 29 outliers final: 17 residues processed: 158 average time/residue: 0.1963 time to fit residues: 41.5900 Evaluate side-chains 143 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7739 Z= 0.235 Angle : 0.756 10.012 10463 Z= 0.377 Chirality : 0.045 0.222 1183 Planarity : 0.005 0.078 1327 Dihedral : 7.410 50.824 1047 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 4.81 % Allowed : 22.84 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.27), residues: 946 helix: -0.84 (0.25), residues: 398 sheet: -3.22 (0.54), residues: 71 loop : -2.53 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 957 HIS 0.005 0.001 HIS A 312 PHE 0.028 0.002 PHE A 811 TYR 0.012 0.002 TYR A 647 ARG 0.004 0.001 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6779 (ptt) REVERT: A 701 MET cc_start: 0.5657 (mmt) cc_final: 0.5364 (mmm) REVERT: A 756 MET cc_start: 0.6797 (ptp) cc_final: 0.6415 (ptp) REVERT: B 162 ILE cc_start: 0.7138 (mp) cc_final: 0.6704 (mp) REVERT: B 213 TYR cc_start: 0.4104 (t80) cc_final: 0.3816 (t80) REVERT: B 265 GLU cc_start: 0.7236 (tt0) cc_final: 0.6703 (tt0) outliers start: 40 outliers final: 31 residues processed: 155 average time/residue: 0.1997 time to fit residues: 41.6999 Evaluate side-chains 151 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.0970 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7739 Z= 0.204 Angle : 0.768 10.910 10463 Z= 0.376 Chirality : 0.044 0.207 1183 Planarity : 0.005 0.092 1327 Dihedral : 7.295 50.769 1047 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 5.05 % Allowed : 25.00 % Favored : 69.95 % 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: -2.61 (0.27), residues: 946 helix: -0.68 (0.26), residues: 402 sheet: -3.18 (0.54), residues: 71 loop : -2.47 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 241 HIS 0.004 0.001 HIS A 782 PHE 0.026 0.001 PHE A 811 TYR 0.022 0.002 TYR B 141 ARG 0.010 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7741 (m90) cc_final: 0.7422 (m90) REVERT: A 424 MET cc_start: 0.8245 (ppp) cc_final: 0.8031 (ppp) REVERT: A 521 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6701 (ptt) REVERT: A 701 MET cc_start: 0.5647 (mmt) cc_final: 0.5338 (mmm) REVERT: A 915 LEU cc_start: 0.8648 (tp) cc_final: 0.8381 (tt) REVERT: B 162 ILE cc_start: 0.7193 (mp) cc_final: 0.6698 (mp) REVERT: B 163 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7152 (mmtm) REVERT: B 213 TYR cc_start: 0.4029 (t80) cc_final: 0.3739 (t80) REVERT: B 265 GLU cc_start: 0.7245 (tt0) cc_final: 0.6772 (tt0) outliers start: 42 outliers final: 27 residues processed: 159 average time/residue: 0.2014 time to fit residues: 42.9724 Evaluate side-chains 148 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 0.0010 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7739 Z= 0.185 Angle : 0.754 10.473 10463 Z= 0.370 Chirality : 0.044 0.198 1183 Planarity : 0.005 0.086 1327 Dihedral : 7.161 59.336 1047 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 4.57 % Allowed : 26.08 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.27), residues: 946 helix: -0.59 (0.26), residues: 406 sheet: -3.04 (0.56), residues: 71 loop : -2.50 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 241 HIS 0.004 0.001 HIS A 782 PHE 0.015 0.001 PHE A 648 TYR 0.037 0.002 TYR A 630 ARG 0.006 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8543 (ttt90) cc_final: 0.8228 (tpt-90) REVERT: A 521 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6534 (ptt) REVERT: A 701 MET cc_start: 0.5619 (mmt) cc_final: 0.5312 (mmm) REVERT: B 162 ILE cc_start: 0.7070 (mp) cc_final: 0.6507 (mp) REVERT: B 163 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7176 (mmtt) REVERT: B 213 TYR cc_start: 0.4019 (t80) cc_final: 0.3733 (t80) REVERT: B 265 GLU cc_start: 0.7410 (tt0) cc_final: 0.6872 (tt0) outliers start: 38 outliers final: 32 residues processed: 155 average time/residue: 0.1905 time to fit residues: 39.9629 Evaluate side-chains 154 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.167 Angle : 0.769 12.603 10463 Z= 0.366 Chirality : 0.044 0.155 1183 Planarity : 0.005 0.079 1327 Dihedral : 6.890 53.155 1047 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.97 % Allowed : 27.64 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.27), residues: 946 helix: -0.37 (0.26), residues: 397 sheet: -2.52 (0.64), residues: 62 loop : -2.56 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 241 HIS 0.003 0.001 HIS A 782 PHE 0.019 0.001 PHE A 811 TYR 0.034 0.001 TYR A 630 ARG 0.010 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7715 (m90) cc_final: 0.6919 (t-90) REVERT: A 488 ARG cc_start: 0.8599 (ttt90) cc_final: 0.8281 (tpt-90) REVERT: A 521 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6514 (ptt) REVERT: A 701 MET cc_start: 0.5556 (mmt) cc_final: 0.5197 (mmm) REVERT: A 915 LEU cc_start: 0.8548 (tp) cc_final: 0.8324 (tt) REVERT: B 162 ILE cc_start: 0.6976 (mp) cc_final: 0.6429 (mp) REVERT: B 163 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7018 (mmtt) REVERT: B 213 TYR cc_start: 0.3995 (t80) cc_final: 0.3739 (t80) outliers start: 33 outliers final: 24 residues processed: 157 average time/residue: 0.2055 time to fit residues: 43.1663 Evaluate side-chains 150 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7739 Z= 0.330 Angle : 0.877 13.528 10463 Z= 0.431 Chirality : 0.049 0.230 1183 Planarity : 0.005 0.076 1327 Dihedral : 7.220 51.149 1044 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.53 % Favored : 85.47 % Rotamer: Outliers : 4.93 % Allowed : 27.76 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.27), residues: 946 helix: -0.73 (0.25), residues: 403 sheet: -3.12 (0.51), residues: 86 loop : -2.50 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 241 HIS 0.007 0.001 HIS A 782 PHE 0.029 0.002 PHE A 648 TYR 0.034 0.002 TYR A 630 ARG 0.004 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7196 (ptt) REVERT: A 701 MET cc_start: 0.5783 (mmt) cc_final: 0.5464 (mmm) REVERT: B 162 ILE cc_start: 0.7235 (mp) cc_final: 0.6586 (mp) REVERT: B 163 LYS cc_start: 0.7698 (mmtt) cc_final: 0.6987 (mmtt) REVERT: B 213 TYR cc_start: 0.4180 (t80) cc_final: 0.3962 (t80) REVERT: B 241 MET cc_start: 0.6086 (ppp) cc_final: 0.5308 (ppp) outliers start: 41 outliers final: 31 residues processed: 154 average time/residue: 0.1895 time to fit residues: 39.9670 Evaluate side-chains 151 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0040 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7739 Z= 0.173 Angle : 0.827 14.039 10463 Z= 0.391 Chirality : 0.046 0.212 1183 Planarity : 0.005 0.083 1327 Dihedral : 6.795 52.931 1044 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.12 % Allowed : 29.81 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.28), residues: 946 helix: -0.43 (0.26), residues: 403 sheet: -2.55 (0.58), residues: 77 loop : -2.43 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 241 HIS 0.004 0.001 HIS B 125 PHE 0.025 0.001 PHE A 811 TYR 0.021 0.002 TYR A 570 ARG 0.006 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8680 (ttt90) cc_final: 0.8287 (tpt-90) REVERT: A 521 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6589 (ptt) REVERT: A 701 MET cc_start: 0.5604 (mmt) cc_final: 0.5236 (mmm) REVERT: B 162 ILE cc_start: 0.7028 (mp) cc_final: 0.6445 (mp) REVERT: B 163 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7085 (mmtt) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.2007 time to fit residues: 40.5556 Evaluate side-chains 147 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 0.0040 chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 58 optimal weight: 0.0870 chunk 46 optimal weight: 0.0070 chunk 59 optimal weight: 0.0470 chunk 80 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7739 Z= 0.170 Angle : 0.850 13.732 10463 Z= 0.390 Chirality : 0.046 0.190 1183 Planarity : 0.005 0.076 1327 Dihedral : 6.329 46.966 1044 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 2.28 % Allowed : 30.53 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 946 helix: -0.28 (0.26), residues: 396 sheet: -2.74 (0.53), residues: 89 loop : -2.31 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 241 HIS 0.012 0.001 HIS B 125 PHE 0.011 0.001 PHE A 640 TYR 0.020 0.001 TYR B 141 ARG 0.005 0.000 ARG B 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8731 (ttt90) cc_final: 0.8448 (tpt-90) REVERT: A 521 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6542 (ptt) REVERT: A 637 GLU cc_start: 0.6331 (tm-30) cc_final: 0.5946 (tm-30) REVERT: A 1007 TYR cc_start: 0.5752 (p90) cc_final: 0.5493 (p90) REVERT: B 162 ILE cc_start: 0.6867 (mp) cc_final: 0.6404 (mp) REVERT: B 163 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6958 (mmtt) REVERT: B 244 TYR cc_start: 0.8504 (t80) cc_final: 0.8190 (t80) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.2012 time to fit residues: 40.8758 Evaluate side-chains 144 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 957 TRP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.106032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085556 restraints weight = 56652.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.089035 restraints weight = 26214.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.091257 restraints weight = 16223.007| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7739 Z= 0.200 Angle : 0.858 13.431 10463 Z= 0.402 Chirality : 0.045 0.168 1183 Planarity : 0.005 0.075 1327 Dihedral : 6.391 47.797 1044 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 2.16 % Allowed : 31.37 % Favored : 66.47 % 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: -2.25 (0.28), residues: 946 helix: -0.34 (0.26), residues: 396 sheet: -2.73 (0.54), residues: 86 loop : -2.30 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 241 HIS 0.012 0.001 HIS B 125 PHE 0.039 0.002 PHE B 142 TYR 0.018 0.001 TYR A 570 ARG 0.004 0.000 ARG A 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.24 seconds wall clock time: 36 minutes 52.17 seconds (2212.17 seconds total)