Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 17:30:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwp_23553/04_2023/7lwp_23553.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 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 101 5.16 5 C 15004 2.51 5 N 3871 2.21 5 O 4523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23499 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7699 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 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': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7697 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 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': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7669 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 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 chiralities: 10 Time building chain proxies: 12.39, per 1000 atoms: 0.53 Number of scatterers: 23499 At special positions: 0 Unit cell: (128.28, 134.694, 196.696, 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 101 16.00 O 4523 8.00 N 3871 7.00 C 15004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " 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 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " Time building additional restraints: 10.34 Conformation dependent library (CDL) restraints added in 3.7 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 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 26.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.898A pdb=" N GLY A 142 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.986A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.645A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.644A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.845A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 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 Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 935 through 940 removed outlier: 3.917A pdb=" N LEU A 938 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.762A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.560A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.333A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.672A pdb=" N VAL B 143 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.529A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.531A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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: 3.812A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.592A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.762A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.907A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (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 965 removed outlier: 3.586A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.862A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.506A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.709A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.513A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.548A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.668A 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 removed outlier: 3.531A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1033 removed outlier: 4.009A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.444A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.078A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.759A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.396A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.202A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.726A 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 removed outlier: 4.137A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.797A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 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: 6.127A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.589A 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 714 removed outlier: 3.672A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 728 removed outlier: 6.003A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.599A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.672A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.172A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.452A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.389A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN B 564 " --> pdb=" O ARG B 577 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 45 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 565 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.762A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.008A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.323A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.503A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.561A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.008A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.933A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 10.065A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 51 removed outlier: 4.012A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.903A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.942A 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 655 removed outlier: 6.620A 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: 6.447A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.447A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1001 hydrogen bonds defined for protein. 2688 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: 12.29 Time building geometry restraints manager: 11.03 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: 6338 1.33 - 1.46: 4384 1.46 - 1.58: 13162 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24009 Sorted by residual: bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.59e+01 bond pdb=" C5 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.34e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 24004 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.61: 344 104.61 - 112.30: 10362 112.30 - 120.00: 11120 120.00 - 127.70: 10716 127.70 - 135.39: 134 Bond angle restraints: 32676 Sorted by residual: angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA PHE B 400 " pdb=" CB PHE B 400 " pdb=" CG PHE B 400 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.31e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 ... (remaining 32671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13018 17.95 - 35.89: 762 35.89 - 53.84: 142 53.84 - 71.78: 51 71.78 - 89.72: 37 Dihedral angle restraints: 14010 sinusoidal: 5349 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.27 75.27 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 151.38 -58.38 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA THR C 599 " pdb=" C THR C 599 " pdb=" N PRO C 600 " pdb=" CA PRO C 600 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2621 0.095 - 0.190: 1064 0.190 - 0.285: 139 0.285 - 0.379: 19 0.379 - 0.474: 5 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CA LEU A 878 " pdb=" N LEU A 878 " pdb=" C LEU A 878 " pdb=" CB LEU A 878 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA GLN A 784 " pdb=" N GLN A 784 " pdb=" C GLN A 784 " pdb=" CB GLN A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LEU B1034 " pdb=" N LEU B1034 " pdb=" C LEU B1034 " pdb=" CB LEU B1034 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 3845 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.344 2.00e-02 2.50e+03 1.84e-01 8.51e+02 pdb=" CG TRP C 886 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.178 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.129 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.270 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.201 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.064 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.130 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" CG ASN C1074 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.123 2.00e-02 2.50e+03 1.40e-01 2.43e+02 pdb=" CG ASN B1074 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.167 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 10839 2.98 - 3.46: 22215 3.46 - 3.94: 38901 3.94 - 4.42: 42895 4.42 - 4.90: 73319 Nonbonded interactions: 188169 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.498 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.521 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.522 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.522 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.523 2.440 ... (remaining 188164 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 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e 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 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 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 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 name O or name CB )) or resid 481 through 487 or (resid 488 and (name N or \ name CA or name C or name O or name CB )) or resid 489 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 n \ ame O or name CB )) or resid 749 through 810 or (resid 811 and (name N or name C \ A or name C or name O or name CB )) or resid 813 through 827 or resid 855 throug \ h 866 or (resid 867 through 868 and (name N or name CA or name C or name O or na \ me CB )) or resid 869 through 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e 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 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 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 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 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 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 11 \ 47 or resid 1301 through 1310)) 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 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 143 or (re \ sid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 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 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 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 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 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 and (name N or name CA or name C or name O or name CB )) or resid 1147 or \ resid 1301 through 1310)) } 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 individual isotropic 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: 1.710 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: 7.930 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 65.640 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 0.074 24009 Z= 0.877 Angle : 1.799 10.392 32676 Z= 1.206 Chirality : 0.096 0.474 3848 Planarity : 0.013 0.189 4178 Dihedral : 13.668 89.725 8319 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.60 % Favored : 93.92 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.29 % 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: -1.08 (0.14), residues: 2928 helix: -1.28 (0.16), residues: 673 sheet: 0.47 (0.22), residues: 483 loop : -0.80 (0.14), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 310 time to evaluate : 2.496 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 outliers start: 29 outliers final: 10 residues processed: 332 average time/residue: 0.3746 time to fit residues: 191.2768 Evaluate side-chains 168 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 2.959 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2261 time to fit residues: 8.1153 ------------------------------------------------------------------------------- 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: 0.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 613 GLN A 824 ASN A 960 ASN A1088 HIS B 613 GLN B 777 ASN B 925 ASN B 935 GLN B 965 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 211 ASN C 703 ASN C 965 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24009 Z= 0.202 Angle : 0.637 9.273 32676 Z= 0.341 Chirality : 0.047 0.210 3848 Planarity : 0.004 0.038 4178 Dihedral : 5.708 26.958 3175 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.48 % Favored : 96.38 % Rotamer Outliers : 1.14 % 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 (0.15), residues: 2928 helix: 0.81 (0.20), residues: 663 sheet: 0.38 (0.19), residues: 648 loop : -0.60 (0.15), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 201 average time/residue: 0.3584 time to fit residues: 117.1615 Evaluate side-chains 144 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 2.548 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2559 time to fit residues: 10.9123 ------------------------------------------------------------------------------- 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: 0.9990 chunk 83 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 613 GLN A 784 GLN A 804 GLN A1048 HIS A1088 HIS B 901 GLN B1005 GLN B1010 GLN B1048 HIS B1064 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 762 GLN C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 24009 Z= 0.238 Angle : 0.582 9.270 32676 Z= 0.306 Chirality : 0.046 0.197 3848 Planarity : 0.004 0.038 4178 Dihedral : 5.095 27.805 3175 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.73 % Rotamer Outliers : 1.49 % 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 (0.15), residues: 2928 helix: 1.12 (0.21), residues: 670 sheet: 0.51 (0.19), residues: 660 loop : -0.52 (0.15), residues: 1598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 177 average time/residue: 0.3225 time to fit residues: 96.1141 Evaluate side-chains 140 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 2.693 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2281 time to fit residues: 11.8423 ------------------------------------------------------------------------------- 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: 0.3980 chunk 203 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 181 optimal weight: 0.0040 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 784 GLN B1005 GLN B1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN C 762 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 24009 Z= 0.230 Angle : 0.553 11.241 32676 Z= 0.287 Chirality : 0.045 0.200 3848 Planarity : 0.004 0.039 4178 Dihedral : 4.820 26.618 3175 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.24 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2928 helix: 1.29 (0.21), residues: 664 sheet: 0.57 (0.19), residues: 646 loop : -0.46 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 159 average time/residue: 0.3306 time to fit residues: 87.4592 Evaluate side-chains 141 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 2.661 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2059 time to fit residues: 8.0845 ------------------------------------------------------------------------------- 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: 0.8980 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 926 GLN B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24009 Z= 0.182 Angle : 0.512 7.313 32676 Z= 0.268 Chirality : 0.044 0.194 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.510 24.348 3175 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.00 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2928 helix: 1.43 (0.21), residues: 675 sheet: 0.56 (0.19), residues: 650 loop : -0.41 (0.16), residues: 1603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 154 average time/residue: 0.3499 time to fit residues: 88.8628 Evaluate side-chains 143 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 2.573 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2143 time to fit residues: 9.8436 ------------------------------------------------------------------------------- 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: 0.9980 chunk 258 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 238 optimal weight: 20.0000 chunk 133 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 87 ASN A 613 GLN A 949 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 24009 Z= 0.277 Angle : 0.565 10.312 32676 Z= 0.292 Chirality : 0.046 0.211 3848 Planarity : 0.004 0.039 4178 Dihedral : 4.652 26.527 3175 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.90 % Rotamer Outliers : 0.71 % 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: 0.22 (0.15), residues: 2928 helix: 1.31 (0.21), residues: 675 sheet: 0.43 (0.19), residues: 662 loop : -0.46 (0.16), residues: 1591 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.3307 time to fit residues: 83.9773 Evaluate side-chains 137 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 2.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2084 time to fit residues: 7.9167 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 241 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 613 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 563 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 24009 Z= 0.161 Angle : 0.499 9.047 32676 Z= 0.259 Chirality : 0.043 0.191 3848 Planarity : 0.003 0.039 4178 Dihedral : 4.324 23.037 3175 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.24 % Rotamer Outliers : 0.59 % 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: 0.39 (0.15), residues: 2928 helix: 1.61 (0.21), residues: 676 sheet: 0.49 (0.19), residues: 659 loop : -0.39 (0.16), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.3317 time to fit residues: 79.8237 Evaluate side-chains 132 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 2.903 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2370 time to fit residues: 7.5801 ------------------------------------------------------------------------------- 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: 4.9990 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 141 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24009 Z= 0.167 Angle : 0.494 8.762 32676 Z= 0.257 Chirality : 0.043 0.194 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.217 22.769 3175 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2928 helix: 1.65 (0.21), residues: 677 sheet: 0.49 (0.19), residues: 671 loop : -0.37 (0.16), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.3339 time to fit residues: 79.1194 Evaluate side-chains 125 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 2.688 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2236 time to fit residues: 6.4242 ------------------------------------------------------------------------------- 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: 1.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 266 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN C 580 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24009 Z= 0.203 Angle : 0.512 9.017 32676 Z= 0.265 Chirality : 0.044 0.201 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.261 23.600 3175 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer Outliers : 0.24 % 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: 0.38 (0.16), residues: 2928 helix: 1.53 (0.21), residues: 683 sheet: 0.53 (0.19), residues: 669 loop : -0.40 (0.16), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 134 average time/residue: 0.3417 time to fit residues: 78.2159 Evaluate side-chains 128 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.684 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2272 time to fit residues: 5.4411 ------------------------------------------------------------------------------- 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: 0.0670 chunk 282 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 196 optimal weight: 0.6980 chunk 295 optimal weight: 0.3980 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 24009 Z= 0.137 Angle : 0.476 8.695 32676 Z= 0.248 Chirality : 0.043 0.187 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.040 21.089 3175 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer Outliers : 0.16 % 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: 0.50 (0.16), residues: 2928 helix: 1.69 (0.21), residues: 680 sheet: 0.53 (0.19), residues: 662 loop : -0.31 (0.16), residues: 1586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 131 average time/residue: 0.3303 time to fit residues: 73.2427 Evaluate side-chains 120 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 2.559 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2082 time to fit residues: 4.3490 ------------------------------------------------------------------------------- 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: 3.9990 chunk 250 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 613 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126263 restraints weight = 31105.704| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.65 r_work: 0.3286 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 24009 Z= 0.319 Angle : 0.576 11.037 32676 Z= 0.297 Chirality : 0.046 0.222 3848 Planarity : 0.004 0.037 4178 Dihedral : 4.470 25.911 3175 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2928 helix: 1.31 (0.21), residues: 682 sheet: 0.46 (0.19), residues: 672 loop : -0.43 (0.16), residues: 1574 =============================================================================== Job complete usr+sys time: 4465.19 seconds wall clock time: 82 minutes 18.62 seconds (4938.62 seconds total)