Starting phenix.real_space_refine on Tue Mar 19 06:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyp_23598/03_2024/7lyp_23598.pdb" } resolution = 4.05 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= 0.001 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 15020 2.51 5 N 3878 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7717 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 12.10, per 1000 atoms: 0.51 Number of scatterers: 23504 At special positions: 0 Unit cell: (129.349, 137.901, 192.42, 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 102 16.00 O 4504 8.00 N 3878 7.00 C 15020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 4.3 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.505A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.424A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.322A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.673A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.868A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.695A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.890A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.597A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.998A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.006A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.767A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.941A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.276A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.603A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.508A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.820A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.831A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.876A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.791A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.749A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.349A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.654A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.995A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.250A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.521A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.524A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.714A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N PHE A 220 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.606A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.582A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.074A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.713A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.097A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.553A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.795A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.339A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.509A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.155A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.995A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.696A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.356A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.710A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2814 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: 10.56 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6097 1.33 - 1.45: 4672 1.45 - 1.58: 13128 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24023 Sorted by residual: bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 24018 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.81: 282 103.81 - 111.76: 9650 111.76 - 119.71: 10417 119.71 - 127.66: 12225 127.66 - 135.61: 127 Bond angle restraints: 32701 Sorted by residual: angle pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " pdb=" CG PHE C 456 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA PHE A 456 " pdb=" CB PHE A 456 " pdb=" CG PHE A 456 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" CA ASP A 571 " pdb=" CB ASP A 571 " pdb=" CG ASP A 571 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" N ASN C 709 " pdb=" CA ASN C 709 " pdb=" C ASN C 709 " ideal model delta sigma weight residual 112.87 119.33 -6.46 1.20e+00 6.94e-01 2.90e+01 ... (remaining 32696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13506 17.65 - 35.30: 915 35.30 - 52.94: 134 52.94 - 70.59: 47 70.59 - 88.24: 29 Dihedral angle restraints: 14631 sinusoidal: 5958 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.50 -71.50 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 156.02 -63.02 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.28 57.28 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2357 0.083 - 0.166: 1253 0.166 - 0.249: 186 0.249 - 0.332: 35 0.332 - 0.416: 7 Chirality restraints: 3838 Sorted by residual: chirality pdb=" CB THR C 523 " pdb=" CA THR C 523 " pdb=" OG1 THR C 523 " pdb=" CG2 THR C 523 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA ASN A 710 " pdb=" N ASN A 710 " pdb=" C ASN A 710 " pdb=" CB ASN A 710 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA SER C 112 " pdb=" N SER C 112 " pdb=" C SER C 112 " pdb=" CB SER C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 3835 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " 0.240 2.00e-02 2.50e+03 1.33e-01 3.51e+02 pdb=" CG TYR C 707 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.138 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN B 331 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.143 2.00e-02 2.50e+03 1.47e-01 2.68e+02 pdb=" CG ASN C 709 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.217 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " 0.178 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12029 2.99 - 3.47: 24261 3.47 - 3.94: 39025 3.94 - 4.42: 43397 4.42 - 4.90: 71642 Nonbonded interactions: 190354 Sorted by model distance: nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.509 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.522 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.548 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.553 2.440 ... (remaining 190349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 527 or (resid 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA o \ r name C or name O or name CB )) or resid 812 through 827 or resid 855 through 8 \ 66 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 or resid 1 \ 301 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 479 or (resid 480 and (name N or name CA or name C or n \ ame O or name CB )) or resid 481 through 567 or (resid 568 and (name N or name C \ A or name C or name O or name CB )) or resid 569 through 582 or (resid 583 and ( \ name N or name CA or name C or name O or name CB )) or resid 584 through 585 or \ (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 and (na \ me N or name CA or name C or name O or name CB )) or resid 869 through 1091 or ( \ resid 1092 and (name N or name CA or name C or name O or name CB )) or resid 109 \ 3 through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 and (name N or name CA or name C or name O \ or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) o \ r resid 529 through 567 or (resid 568 and (name N or name CA or name C or name O \ or name CB )) or resid 569 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 618 or (resi \ d 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1308) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.020 Extract box with map and model: 7.000 Check model and map are aligned: 0.720 Set scattering table: 0.280 Process input model: 65.180 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.075 24023 Z= 0.841 Angle : 1.732 9.347 32701 Z= 1.149 Chirality : 0.093 0.416 3838 Planarity : 0.015 0.150 4181 Dihedral : 12.971 88.242 8940 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.67 % Favored : 92.71 % Rotamer: Outliers : 0.71 % Allowed : 2.04 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 2937 helix: -0.65 (0.17), residues: 686 sheet: 0.47 (0.24), residues: 417 loop : -1.21 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.021 TRP A 436 HIS 0.023 0.004 HIS B1048 PHE 0.088 0.013 PHE A1095 TYR 0.240 0.023 TYR C 707 ARG 0.013 0.002 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 2.569 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: A 297 SER cc_start: 0.8929 (m) cc_final: 0.8710 (p) REVERT: A 512 VAL cc_start: 0.9112 (t) cc_final: 0.8859 (p) REVERT: A 557 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7286 (mmtm) REVERT: B 63 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.7950 (p) REVERT: B 198 ASP cc_start: 0.9050 (m-30) cc_final: 0.8628 (p0) REVERT: B 223 LEU cc_start: 0.8738 (mp) cc_final: 0.8447 (mp) REVERT: B 238 PHE cc_start: 0.8800 (p90) cc_final: 0.8540 (p90) REVERT: B 365 TYR cc_start: 0.9333 (m-80) cc_final: 0.9102 (m-80) REVERT: B 427 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: B 650 LEU cc_start: 0.9340 (tp) cc_final: 0.9028 (tt) REVERT: B 864 LEU cc_start: 0.8853 (tp) cc_final: 0.8439 (tp) REVERT: C 509 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7420 (mtp85) REVERT: C 611 LEU cc_start: 0.9210 (tp) cc_final: 0.9006 (tt) REVERT: C 613 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: C 902 MET cc_start: 0.9568 (mmm) cc_final: 0.9366 (tpp) outliers start: 18 outliers final: 4 residues processed: 252 average time/residue: 0.3367 time to fit residues: 132.9437 Evaluate side-chains 116 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1135 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 498 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24023 Z= 0.262 Angle : 0.674 9.975 32701 Z= 0.361 Chirality : 0.047 0.286 3838 Planarity : 0.004 0.065 4181 Dihedral : 7.208 57.309 3776 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2937 helix: 1.17 (0.20), residues: 667 sheet: 0.16 (0.21), residues: 542 loop : -0.88 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 64 HIS 0.006 0.001 HIS B 66 PHE 0.026 0.002 PHE C 906 TYR 0.023 0.002 TYR B 200 ARG 0.006 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8911 (m) cc_final: 0.8699 (p) REVERT: A 456 PHE cc_start: 0.8820 (p90) cc_final: 0.8586 (p90) REVERT: A 557 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7279 (mmtm) REVERT: B 56 LEU cc_start: 0.8769 (tp) cc_final: 0.8496 (tp) REVERT: B 90 VAL cc_start: 0.9242 (t) cc_final: 0.8870 (m) REVERT: B 91 TYR cc_start: 0.7833 (t80) cc_final: 0.7451 (t80) REVERT: B 650 LEU cc_start: 0.9403 (tp) cc_final: 0.9084 (tt) REVERT: B 864 LEU cc_start: 0.8843 (tp) cc_final: 0.8604 (tp) REVERT: B 1002 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8244 (tm-30) REVERT: B 1005 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 395 VAL cc_start: 0.8283 (m) cc_final: 0.7932 (p) REVERT: C 417 ASN cc_start: 0.9384 (m110) cc_final: 0.9011 (p0) REVERT: C 509 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7721 (mtp85) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.3453 time to fit residues: 90.2405 Evaluate side-chains 92 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 270 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 498 GLN B 955 ASN B1119 ASN C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24023 Z= 0.195 Angle : 0.585 7.892 32701 Z= 0.310 Chirality : 0.044 0.260 3838 Planarity : 0.004 0.065 4181 Dihedral : 6.344 55.831 3776 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.02 (0.15), residues: 2937 helix: 1.60 (0.20), residues: 671 sheet: 0.09 (0.20), residues: 585 loop : -0.66 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.027 0.001 PHE C 559 TYR 0.033 0.002 TYR B 505 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9026 (mm) cc_final: 0.8344 (tp) REVERT: A 168 PHE cc_start: 0.8316 (t80) cc_final: 0.7966 (t80) REVERT: A 297 SER cc_start: 0.8913 (m) cc_final: 0.8630 (p) REVERT: A 557 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7310 (mmtm) REVERT: B 90 VAL cc_start: 0.9119 (t) cc_final: 0.8839 (t) REVERT: B 91 TYR cc_start: 0.7752 (t80) cc_final: 0.7439 (t80) REVERT: B 238 PHE cc_start: 0.8686 (p90) cc_final: 0.8300 (p90) REVERT: B 1005 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 395 VAL cc_start: 0.8167 (m) cc_final: 0.7880 (p) REVERT: C 417 ASN cc_start: 0.9387 (m110) cc_final: 0.9007 (p0) REVERT: C 509 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7397 (mtp85) REVERT: C 611 LEU cc_start: 0.9084 (tp) cc_final: 0.8862 (tt) REVERT: C 699 LEU cc_start: 0.8982 (mt) cc_final: 0.8738 (mp) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.3276 time to fit residues: 79.8093 Evaluate side-chains 86 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 710 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24023 Z= 0.340 Angle : 0.646 9.755 32701 Z= 0.337 Chirality : 0.045 0.240 3838 Planarity : 0.004 0.063 4181 Dihedral : 6.473 55.884 3776 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2937 helix: 1.30 (0.20), residues: 669 sheet: -0.09 (0.20), residues: 607 loop : -0.79 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.008 0.001 HIS A1048 PHE 0.028 0.002 PHE C 342 TYR 0.027 0.002 TYR B 505 ARG 0.007 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.471 Fit side-chains REVERT: A 297 SER cc_start: 0.8946 (m) cc_final: 0.8674 (p) REVERT: A 354 ASN cc_start: 0.8629 (m-40) cc_final: 0.8335 (m-40) REVERT: A 456 PHE cc_start: 0.8900 (p90) cc_final: 0.8479 (p90) REVERT: A 473 TYR cc_start: 0.7051 (t80) cc_final: 0.6514 (t80) REVERT: A 557 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7338 (mmtm) REVERT: B 52 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 56 LEU cc_start: 0.8863 (tp) cc_final: 0.8438 (tp) REVERT: B 1005 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 395 VAL cc_start: 0.8087 (m) cc_final: 0.7878 (p) REVERT: C 417 ASN cc_start: 0.9433 (m110) cc_final: 0.9026 (p0) REVERT: C 611 LEU cc_start: 0.9093 (tp) cc_final: 0.8865 (tt) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.3054 time to fit residues: 59.2036 Evaluate side-chains 75 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 213 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24023 Z= 0.317 Angle : 0.616 9.584 32701 Z= 0.322 Chirality : 0.045 0.251 3838 Planarity : 0.004 0.053 4181 Dihedral : 6.378 54.884 3776 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.15), residues: 2937 helix: 1.37 (0.20), residues: 676 sheet: -0.13 (0.19), residues: 628 loop : -0.88 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.008 0.001 HIS A1048 PHE 0.025 0.002 PHE C 342 TYR 0.026 0.002 TYR B 200 ARG 0.007 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 2.673 Fit side-chains REVERT: A 168 PHE cc_start: 0.8240 (t80) cc_final: 0.8008 (t80) REVERT: A 297 SER cc_start: 0.9001 (m) cc_final: 0.8725 (p) REVERT: A 354 ASN cc_start: 0.8649 (m-40) cc_final: 0.8347 (m-40) REVERT: A 456 PHE cc_start: 0.8959 (p90) cc_final: 0.8531 (p90) REVERT: A 473 TYR cc_start: 0.7286 (t80) cc_final: 0.6655 (t80) REVERT: A 557 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7414 (mmtm) REVERT: A 979 ASP cc_start: 0.8797 (m-30) cc_final: 0.8518 (t0) REVERT: B 52 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 805 ILE cc_start: 0.9561 (pt) cc_final: 0.9319 (mt) REVERT: B 1005 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 395 VAL cc_start: 0.8038 (m) cc_final: 0.7669 (p) REVERT: C 417 ASN cc_start: 0.9431 (m110) cc_final: 0.9006 (p0) REVERT: C 509 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7005 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.3180 time to fit residues: 59.7881 Evaluate side-chains 77 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 287 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 23 optimal weight: 0.0030 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24023 Z= 0.160 Angle : 0.525 7.094 32701 Z= 0.277 Chirality : 0.044 0.359 3838 Planarity : 0.004 0.051 4181 Dihedral : 5.910 53.498 3776 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 0.04 % Allowed : 1.14 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.01 (0.15), residues: 2937 helix: 1.87 (0.21), residues: 655 sheet: 0.03 (0.20), residues: 617 loop : -0.77 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.003 0.001 HIS A 655 PHE 0.036 0.001 PHE A 559 TYR 0.021 0.001 TYR B 200 ARG 0.004 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 2.600 Fit side-chains REVERT: A 168 PHE cc_start: 0.8139 (t80) cc_final: 0.7896 (t80) REVERT: A 297 SER cc_start: 0.8950 (m) cc_final: 0.8685 (p) REVERT: A 456 PHE cc_start: 0.8877 (p90) cc_final: 0.8526 (p90) REVERT: A 473 TYR cc_start: 0.7367 (t80) cc_final: 0.6798 (t80) REVERT: A 557 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7371 (mmtm) REVERT: B 52 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 864 LEU cc_start: 0.8863 (tp) cc_final: 0.8610 (tp) REVERT: B 1002 GLN cc_start: 0.8639 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 1005 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 297 SER cc_start: 0.9397 (m) cc_final: 0.9190 (p) REVERT: C 395 VAL cc_start: 0.8183 (m) cc_final: 0.7852 (p) REVERT: C 417 ASN cc_start: 0.9393 (m110) cc_final: 0.8985 (p0) REVERT: C 509 ARG cc_start: 0.7895 (mtt180) cc_final: 0.6960 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3156 time to fit residues: 64.2520 Evaluate side-chains 81 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24023 Z= 0.338 Angle : 0.616 9.647 32701 Z= 0.320 Chirality : 0.045 0.284 3838 Planarity : 0.004 0.053 4181 Dihedral : 6.180 54.650 3776 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 0.04 % Allowed : 0.82 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.19 (0.15), residues: 2937 helix: 1.49 (0.20), residues: 661 sheet: -0.00 (0.20), residues: 624 loop : -0.85 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.008 0.001 HIS A1048 PHE 0.032 0.002 PHE A 559 TYR 0.022 0.002 TYR B 200 ARG 0.010 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.844 Fit side-chains REVERT: A 168 PHE cc_start: 0.8156 (t80) cc_final: 0.7930 (t80) REVERT: A 297 SER cc_start: 0.9040 (m) cc_final: 0.8726 (p) REVERT: A 456 PHE cc_start: 0.8888 (p90) cc_final: 0.8581 (p90) REVERT: A 473 TYR cc_start: 0.7675 (t80) cc_final: 0.7069 (t80) REVERT: B 52 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 547 THR cc_start: 0.8817 (p) cc_final: 0.8535 (p) REVERT: B 1005 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 395 VAL cc_start: 0.8100 (m) cc_final: 0.7769 (p) REVERT: C 417 ASN cc_start: 0.9436 (m110) cc_final: 0.8996 (p0) REVERT: C 509 ARG cc_start: 0.7876 (mtt180) cc_final: 0.6926 (mtp85) REVERT: C 528 LYS cc_start: 0.8753 (ptmt) cc_final: 0.8484 (pttm) REVERT: C 968 SER cc_start: 0.9311 (m) cc_final: 0.9100 (t) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.3151 time to fit residues: 56.5956 Evaluate side-chains 77 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 170 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.0470 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 81 ASN B1083 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24023 Z= 0.172 Angle : 0.532 18.554 32701 Z= 0.274 Chirality : 0.044 0.272 3838 Planarity : 0.004 0.050 4181 Dihedral : 5.767 53.143 3776 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2937 helix: 1.84 (0.21), residues: 654 sheet: 0.09 (0.20), residues: 628 loop : -0.74 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE A 559 TYR 0.020 0.001 TYR B 200 ARG 0.007 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8141 (t80) cc_final: 0.7890 (t80) REVERT: A 297 SER cc_start: 0.8988 (m) cc_final: 0.8662 (p) REVERT: A 557 LYS cc_start: 0.7403 (mmtm) cc_final: 0.7087 (mmtm) REVERT: B 52 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 238 PHE cc_start: 0.8844 (p90) cc_final: 0.8517 (p90) REVERT: B 864 LEU cc_start: 0.8883 (tp) cc_final: 0.8605 (tp) REVERT: B 1002 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 1005 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 395 VAL cc_start: 0.8216 (m) cc_final: 0.7867 (p) REVERT: C 417 ASN cc_start: 0.9413 (m110) cc_final: 0.8985 (p0) REVERT: C 509 ARG cc_start: 0.7839 (mtt180) cc_final: 0.6874 (mtp85) REVERT: C 528 LYS cc_start: 0.8688 (ptmt) cc_final: 0.8423 (pttm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3329 time to fit residues: 60.6531 Evaluate side-chains 77 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 chunk 250 optimal weight: 0.0970 chunk 266 optimal weight: 0.1980 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24023 Z= 0.166 Angle : 0.510 11.033 32701 Z= 0.266 Chirality : 0.043 0.246 3838 Planarity : 0.004 0.050 4181 Dihedral : 5.589 53.588 3776 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2937 helix: 1.88 (0.21), residues: 655 sheet: 0.19 (0.20), residues: 625 loop : -0.70 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE C 906 TYR 0.019 0.001 TYR B 200 ARG 0.007 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.872 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8061 (t80) cc_final: 0.7846 (t80) REVERT: A 297 SER cc_start: 0.8987 (m) cc_final: 0.8646 (p) REVERT: A 557 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7111 (mmtm) REVERT: B 52 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 1005 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 395 VAL cc_start: 0.8260 (m) cc_final: 0.7967 (p) REVERT: C 417 ASN cc_start: 0.9431 (m110) cc_final: 0.9012 (p0) REVERT: C 509 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6871 (mtp85) REVERT: C 528 LYS cc_start: 0.8791 (ptmt) cc_final: 0.8484 (pttm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3251 time to fit residues: 59.0070 Evaluate side-chains 74 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.8980 chunk 282 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 0.0970 chunk 144 optimal weight: 9.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24023 Z= 0.191 Angle : 0.522 7.248 32701 Z= 0.272 Chirality : 0.043 0.279 3838 Planarity : 0.004 0.057 4181 Dihedral : 5.560 53.587 3776 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2937 helix: 1.83 (0.21), residues: 655 sheet: 0.19 (0.20), residues: 645 loop : -0.70 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE C 906 TYR 0.043 0.001 TYR A 266 ARG 0.007 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.929 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8069 (t80) cc_final: 0.7857 (t80) REVERT: A 297 SER cc_start: 0.9004 (m) cc_final: 0.8654 (p) REVERT: A 557 LYS cc_start: 0.7490 (mmtm) cc_final: 0.7154 (mmtm) REVERT: B 52 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 1005 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 395 VAL cc_start: 0.8258 (m) cc_final: 0.7954 (p) REVERT: C 417 ASN cc_start: 0.9446 (m110) cc_final: 0.9025 (p0) REVERT: C 509 ARG cc_start: 0.7840 (mtt180) cc_final: 0.6869 (mtp85) REVERT: C 528 LYS cc_start: 0.8762 (ptmt) cc_final: 0.8528 (pttm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3266 time to fit residues: 55.2870 Evaluate side-chains 69 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 0.0770 chunk 235 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.070297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051068 restraints weight = 123576.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052148 restraints weight = 71563.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052720 restraints weight = 44418.673| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24023 Z= 0.257 Angle : 0.554 7.465 32701 Z= 0.288 Chirality : 0.044 0.278 3838 Planarity : 0.004 0.058 4181 Dihedral : 5.746 54.013 3776 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2937 helix: 1.68 (0.21), residues: 656 sheet: 0.16 (0.20), residues: 652 loop : -0.77 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 64 HIS 0.005 0.001 HIS A1048 PHE 0.025 0.002 PHE C 906 TYR 0.029 0.002 TYR A 473 ARG 0.008 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.87 seconds wall clock time: 61 minutes 57.00 seconds (3717.00 seconds total)