Starting phenix.real_space_refine (version: dev) on Wed Feb 22 10:27:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5v_21549/02_2023/6w5v_21549_updated.pdb" } resolution = 4.0 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. 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 GLU 164": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 989": "NH1" <-> "NH2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A GLU 1185": "OE1" <-> "OE2" Residue "A GLU 1188": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1022 Classifications: {'peptide': 132} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 118} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.62, per 1000 atoms: 0.63 Number of scatterers: 10586 At special positions: 0 Unit cell: (135.908, 95.804, 153.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1988 8.00 N 1665 7.00 C 6855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.06 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.06 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 99 " distance=2.02 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 Links applied BETA1-3 " NAG C 2 " - " BMA C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1413 " - " ASN A 961 " " NAG A1414 " - " ASN A 968 " " NAG A1415 " - " ASN A1064 " " NAG A1418 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 931 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN D 58 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 47.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 88 through 96 removed outlier: 4.958A pdb=" N ARG A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.896A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 186 through 194 removed outlier: 4.246A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 269 through 294 removed outlier: 4.170A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.599A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.750A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.536A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.759A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 575 through 593 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 621 through 638 Processing helix chain 'A' and resid 654 through 678 Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 721 through 749 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 755 through 790 removed outlier: 4.104A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1083 through 1088 removed outlier: 4.183A pdb=" N VAL A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1121 through 1145 Processing helix chain 'A' and resid 1151 through 1176 removed outlier: 3.889A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1201 removed outlier: 4.153A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1213 Processing helix chain 'A' and resid 1220 through 1251 removed outlier: 4.645A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1244 " --> pdb=" O GLY A1240 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing helix chain 'D' and resid 92 through 95 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 208 removed outlier: 5.714A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 404 through 410 Processing sheet with id= D, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 3.661A pdb=" N THR A1036 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1038 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 48 through 50 removed outlier: 8.583A pdb=" N LEU D 49 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN D 146 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 125 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 106 through 115 removed outlier: 5.511A pdb=" N THR D 62 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE D 34 " --> pdb=" O THR D 62 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1335 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: 3.50 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3278 1.35 - 1.48: 2881 1.48 - 1.61: 4596 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 10863 Sorted by residual: bond pdb=" CA LEU A 748 " pdb=" C LEU A 748 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.36e-02 5.41e+03 3.02e+01 bond pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 1.524 1.574 -0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" CA ALA A1017 " pdb=" C ALA A1017 " ideal model delta sigma weight residual 1.522 1.474 0.049 1.37e-02 5.33e+03 1.26e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.334 1.297 0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" C MET A 754 " pdb=" N PRO A 755 " ideal model delta sigma weight residual 1.335 1.295 0.040 1.28e-02 6.10e+03 9.61e+00 ... (remaining 10858 not shown) Histogram of bond angle deviations from ideal: 92.89 - 101.36: 32 101.36 - 109.83: 1959 109.83 - 118.30: 6549 118.30 - 126.77: 6133 126.77 - 135.24: 141 Bond angle restraints: 14814 Sorted by residual: angle pdb=" N ASP A 551 " pdb=" CA ASP A 551 " pdb=" C ASP A 551 " ideal model delta sigma weight residual 112.72 126.58 -13.86 1.14e+00 7.69e-01 1.48e+02 angle pdb=" N THR A 777 " pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 111.14 123.53 -12.39 1.08e+00 8.57e-01 1.32e+02 angle pdb=" N ARG A 789 " pdb=" CA ARG A 789 " pdb=" C ARG A 789 " ideal model delta sigma weight residual 111.28 123.10 -11.82 1.09e+00 8.42e-01 1.18e+02 angle pdb=" C ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta sigma weight residual 111.78 135.24 -23.46 2.20e+00 2.07e-01 1.14e+02 angle pdb=" N ILE A1202 " pdb=" CA ILE A1202 " pdb=" C ILE A1202 " ideal model delta sigma weight residual 110.72 121.40 -10.68 1.01e+00 9.80e-01 1.12e+02 ... (remaining 14809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 5837 24.02 - 48.05: 411 48.05 - 72.07: 109 72.07 - 96.09: 19 96.09 - 120.11: 10 Dihedral angle restraints: 6386 sinusoidal: 2579 harmonic: 3807 Sorted by residual: dihedral pdb=" C ARG A 372 " pdb=" N ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta harmonic sigma weight residual -122.60 -147.37 24.77 0 2.50e+00 1.60e-01 9.82e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 4.05 88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS D 42 " pdb=" SG CYS D 42 " pdb=" SG CYS D 47 " pdb=" CB CYS D 47 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 ... (remaining 6383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.912: 1732 0.912 - 1.824: 1 1.824 - 2.736: 1 2.736 - 3.648: 0 3.648 - 4.560: 2 Chirality restraints: 1736 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.16 -4.56 2.00e-02 2.50e+03 5.20e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 1.94 -4.34 2.00e-02 2.50e+03 4.72e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-02 2.50e+03 1.59e+03 ... (remaining 1733 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.340 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG F 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.283 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG E 2 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 58 " 0.226 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" CG ASN D 58 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN D 58 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN D 58 " -0.368 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.269 2.00e-02 2.50e+03 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 113 2.56 - 3.15: 9978 3.15 - 3.73: 16487 3.73 - 4.32: 22756 4.32 - 4.90: 36264 Nonbonded interactions: 85598 Sorted by model distance: nonbonded pdb=" OG SER A 741 " pdb=" CD1 ILE A1109 " model vdw 1.979 3.460 nonbonded pdb=" N VAL D 33 " pdb=" O THR D 62 " model vdw 2.030 2.520 nonbonded pdb=" O VAL D 33 " pdb=" N THR D 62 " model vdw 2.049 2.520 nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.053 2.440 nonbonded pdb=" O ASP A 501 " pdb=" O PHE A 504 " model vdw 2.074 3.040 ... (remaining 85593 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6855 2.51 5 N 1665 2.21 5 O 1988 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.160 Process input model: 32.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.008 0.075 10863 Z= 0.497 Angle : 1.353 23.460 14814 Z= 0.850 Chirality : 0.184 4.560 1736 Planarity : 0.012 0.287 1851 Dihedral : 17.760 120.112 3882 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 62.54 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.02 % Favored : 92.29 % Rotamer Outliers : 9.99 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.21 (0.22), residues: 1297 helix: -0.45 (0.21), residues: 594 sheet: -1.27 (0.43), residues: 133 loop : -2.65 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 335 time to evaluate : 1.188 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: 114 outliers final: 28 residues processed: 398 average time/residue: 0.2218 time to fit residues: 123.8606 Evaluate side-chains 228 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1710 time to fit residues: 8.8597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 41 ASN A 86 ASN A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 578 GLN A 614 ASN A 641 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A 988 GLN A1046 GLN A1170 HIS ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 66 GLN D 150 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 10863 Z= 0.298 Angle : 0.882 11.977 14814 Z= 0.455 Chirality : 0.054 0.567 1736 Planarity : 0.006 0.068 1851 Dihedral : 9.670 107.990 1551 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.34 (0.23), residues: 1297 helix: 0.22 (0.20), residues: 595 sheet: -1.04 (0.43), residues: 143 loop : -2.09 (0.25), residues: 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 1.296 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 outliers start: 48 outliers final: 24 residues processed: 289 average time/residue: 0.2014 time to fit residues: 87.6977 Evaluate side-chains 220 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1153 time to fit residues: 6.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 10863 Z= 0.308 Angle : 0.790 9.693 14814 Z= 0.407 Chirality : 0.051 0.599 1736 Planarity : 0.005 0.057 1851 Dihedral : 9.897 109.825 1551 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.63 % Favored : 93.29 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.93 (0.23), residues: 1297 helix: 0.48 (0.21), residues: 606 sheet: -0.69 (0.45), residues: 140 loop : -1.86 (0.26), residues: 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 237 average time/residue: 0.1790 time to fit residues: 65.8600 Evaluate side-chains 212 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1082 time to fit residues: 8.2948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 10863 Z= 0.244 Angle : 0.746 11.706 14814 Z= 0.381 Chirality : 0.049 0.596 1736 Planarity : 0.005 0.051 1851 Dihedral : 9.820 109.157 1551 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.80 (0.23), residues: 1297 helix: 0.60 (0.21), residues: 603 sheet: -0.79 (0.42), residues: 147 loop : -1.74 (0.26), residues: 547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 223 average time/residue: 0.1738 time to fit residues: 60.8383 Evaluate side-chains 196 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1069 time to fit residues: 5.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 10863 Z= 0.256 Angle : 0.765 12.568 14814 Z= 0.388 Chirality : 0.049 0.601 1736 Planarity : 0.005 0.049 1851 Dihedral : 9.918 108.946 1551 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.73 (0.23), residues: 1297 helix: 0.63 (0.21), residues: 608 sheet: -0.74 (0.42), residues: 147 loop : -1.69 (0.26), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 206 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 outliers start: 28 outliers final: 12 residues processed: 222 average time/residue: 0.1996 time to fit residues: 68.2538 Evaluate side-chains 191 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1019 time to fit residues: 3.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 10863 Z= 0.402 Angle : 0.807 11.131 14814 Z= 0.422 Chirality : 0.052 0.651 1736 Planarity : 0.005 0.059 1851 Dihedral : 9.991 109.132 1551 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 3.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.95 (0.23), residues: 1297 helix: 0.40 (0.20), residues: 616 sheet: -0.84 (0.41), residues: 146 loop : -1.77 (0.26), residues: 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 1.398 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 outliers start: 43 outliers final: 31 residues processed: 206 average time/residue: 0.1958 time to fit residues: 62.4157 Evaluate side-chains 202 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1019 time to fit residues: 7.1626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 10863 Z= 0.218 Angle : 0.748 12.904 14814 Z= 0.378 Chirality : 0.049 0.626 1736 Planarity : 0.005 0.054 1851 Dihedral : 9.846 108.402 1551 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.78 (0.23), residues: 1297 helix: 0.58 (0.21), residues: 620 sheet: -0.76 (0.41), residues: 147 loop : -1.77 (0.26), residues: 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 207 average time/residue: 0.1804 time to fit residues: 57.3280 Evaluate side-chains 188 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1099 time to fit residues: 3.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 10863 Z= 0.213 Angle : 0.741 13.156 14814 Z= 0.373 Chirality : 0.048 0.610 1736 Planarity : 0.005 0.055 1851 Dihedral : 9.705 108.403 1551 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.60 (0.23), residues: 1297 helix: 0.70 (0.21), residues: 614 sheet: -0.64 (0.41), residues: 147 loop : -1.60 (0.27), residues: 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 204 average time/residue: 0.1852 time to fit residues: 57.8980 Evaluate side-chains 191 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1005 time to fit residues: 3.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 10863 Z= 0.228 Angle : 0.770 13.355 14814 Z= 0.380 Chirality : 0.049 0.607 1736 Planarity : 0.005 0.052 1851 Dihedral : 9.706 108.407 1551 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1297 helix: 0.66 (0.21), residues: 613 sheet: -0.51 (0.42), residues: 147 loop : -1.52 (0.27), residues: 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 196 average time/residue: 0.1892 time to fit residues: 57.2976 Evaluate side-chains 189 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1144 time to fit residues: 3.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 0.0470 chunk 10 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 10863 Z= 0.201 Angle : 0.761 13.618 14814 Z= 0.375 Chirality : 0.048 0.592 1736 Planarity : 0.005 0.052 1851 Dihedral : 9.682 108.110 1551 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.46 (0.24), residues: 1297 helix: 0.75 (0.21), residues: 614 sheet: -0.48 (0.43), residues: 148 loop : -1.48 (0.27), residues: 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 205 average time/residue: 0.2056 time to fit residues: 64.7576 Evaluate side-chains 187 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1023 time to fit residues: 2.2783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 ASN ** 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 = 0.3703 r_free = 0.3703 target = 0.100840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079002 restraints weight = 32288.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081457 restraints weight = 16670.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.083009 restraints weight = 10783.097| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 10863 Z= 0.205 Angle : 0.770 16.843 14814 Z= 0.377 Chirality : 0.048 0.577 1736 Planarity : 0.005 0.088 1851 Dihedral : 9.665 108.320 1551 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.42 (0.24), residues: 1297 helix: 0.72 (0.21), residues: 620 sheet: -0.36 (0.43), residues: 148 loop : -1.43 (0.27), residues: 529 =============================================================================== Job complete usr+sys time: 2164.57 seconds wall clock time: 40 minutes 10.79 seconds (2410.79 seconds total)