Starting phenix.real_space_refine (version: dev) on Wed Feb 22 10:16:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy6_27068/02_2023/8cy6_27068.pdb" } resolution = 3.2 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 868": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 56077 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 16902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16902 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 16900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16900 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 16902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16902 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1791 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1791 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1791 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Time building chain proxies: 18.67, per 1000 atoms: 0.33 Number of scatterers: 56077 At special positions: 0 Unit cell: (168.783, 171.441, 200.679, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 5457 8.00 N 4794 7.00 C 18039 6.00 H 27658 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS F 111 " 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 Time building additional restraints: 33.30 Conformation dependent library (CDL) restraints added in 3.5 seconds 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 62 sheets defined 23.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.960A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.594A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.102A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.114A 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 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.956A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 827 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.814A pdb=" N LYS A 854 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 856' 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 912 through 919 removed outlier: 3.948A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.916A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.163A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.957A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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 1140 through 1146 removed outlier: 4.436A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.381A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.527A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.986A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.122A 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 438 through 443 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.869A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.513A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.649A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.895A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.966A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.091A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.154A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.887A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (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 1140 through 1146 removed outlier: 4.407A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.703A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.596A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.944A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.101A 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 619 through 623 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.837A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 818 through 827 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.699A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 856' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.957A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.083A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.185A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.785A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.508A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'F' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.808A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.808A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.546A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.998A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.654A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 160 removed outlier: 3.528A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 12.626A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.366A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.508A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.667A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.424A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.410A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.410A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.543A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.259A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.947A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.947A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.953A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.531A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 151 through 160 removed outlier: 6.532A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.019A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.449A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.631A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.729A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.624A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.416A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.575A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.901A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.901A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.717A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 151 through 160 removed outlier: 3.585A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 12.740A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.346A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.535A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.710A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.404A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.380A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.296A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AG1, first strand: chain 'D' and resid 27 through 29 removed outlier: 4.018A pdb=" N SER D 135 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 49 " --> pdb=" O ARG D 114 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU D 116 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU D 47 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 65 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 54 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU D 63 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 27 through 29 removed outlier: 4.018A pdb=" N SER D 135 " --> pdb=" O VAL D 28 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AG4, first strand: chain 'E' and resid 27 through 29 removed outlier: 4.143A pdb=" N SER E 135 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU E 116 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU E 47 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN E 48 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER E 68 " --> pdb=" O ASN E 48 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET E 50 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER E 66 " --> pdb=" O MET E 50 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP E 52 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 27 through 29 removed outlier: 4.143A pdb=" N SER E 135 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AG7, first strand: chain 'F' and resid 27 through 29 removed outlier: 3.979A pdb=" N SER F 135 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU F 116 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 47 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 65 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG F 54 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU F 63 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 27 through 29 removed outlier: 3.979A pdb=" N SER F 135 " --> pdb=" O VAL F 28 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3321 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: 22.46 Time building geometry restraints manager: 35.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 27637 1.04 - 1.24: 3492 1.24 - 1.44: 9288 1.44 - 1.64: 16140 1.64 - 1.84: 165 Bond restraints: 56722 Sorted by residual: bond pdb=" N VAL C 622 " pdb=" CA VAL C 622 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.24e+00 bond pdb=" N THR B 531 " pdb=" CA THR B 531 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.95e+00 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.17e+00 bond pdb=" N VAL B 622 " pdb=" CA VAL B 622 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.41e-02 5.03e+03 7.08e+00 bond pdb=" N VAL C 620 " pdb=" H VAL C 620 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 56717 not shown) Histogram of bond angle deviations from ideal: 79.67 - 90.55: 4 90.55 - 101.42: 26 101.42 - 112.30: 64170 112.30 - 123.18: 32350 123.18 - 134.06: 5543 Bond angle restraints: 102093 Sorted by residual: angle pdb=" CB VAL B 159 " pdb=" CG1 VAL B 159 " pdb="HG12 VAL B 159 " ideal model delta sigma weight residual 109.00 79.67 29.33 3.00e+00 1.11e-01 9.56e+01 angle pdb="HG11 VAL B 159 " pdb=" CG1 VAL B 159 " pdb="HG12 VAL B 159 " ideal model delta sigma weight residual 110.00 80.70 29.30 3.00e+00 1.11e-01 9.54e+01 angle pdb="HG11 VAL B 159 " pdb=" CG1 VAL B 159 " pdb="HG13 VAL B 159 " ideal model delta sigma weight residual 110.00 80.98 29.02 3.00e+00 1.11e-01 9.36e+01 angle pdb=" CB VAL B 159 " pdb=" CG1 VAL B 159 " pdb="HG13 VAL B 159 " ideal model delta sigma weight residual 109.00 80.46 28.54 3.00e+00 1.11e-01 9.05e+01 angle pdb="HG12 VAL B 159 " pdb=" CG1 VAL B 159 " pdb="HG13 VAL B 159 " ideal model delta sigma weight residual 110.00 133.80 -23.80 3.00e+00 1.11e-01 6.29e+01 ... (remaining 102088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 21870 17.65 - 35.29: 1024 35.29 - 52.94: 145 52.94 - 70.58: 29 70.58 - 88.23: 36 Dihedral angle restraints: 23104 sinusoidal: 10432 harmonic: 12672 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 -134.62 48.62 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -130.98 44.98 1 1.00e+01 1.00e-02 2.81e+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 93.00 135.57 -42.57 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 23101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3444 0.040 - 0.080: 615 0.080 - 0.119: 362 0.119 - 0.159: 60 0.159 - 0.199: 7 Chirality restraints: 4488 Sorted by residual: chirality pdb=" CA VAL C 622 " pdb=" N VAL C 622 " pdb=" C VAL C 622 " pdb=" CB VAL C 622 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL B 622 " pdb=" N VAL B 622 " pdb=" C VAL B 622 " pdb=" CB VAL B 622 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA THR C 333 " pdb=" N THR C 333 " pdb=" C THR C 333 " pdb=" CB THR C 333 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 4485 not shown) Planarity restraints: 8626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 532 " -0.043 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CG ASN B 532 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 532 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN B 532 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 532 " 0.761 2.00e-02 2.50e+03 pdb="HD22 ASN B 532 " -0.763 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 532 " -0.236 2.00e-02 2.50e+03 2.80e-01 1.17e+03 pdb=" CG ASN A 532 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 532 " 0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN A 532 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 532 " 0.420 2.00e-02 2.50e+03 pdb="HD22 ASN A 532 " -0.431 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.224 2.00e-02 2.50e+03 2.61e-01 1.02e+03 pdb=" CG ASN C 616 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.216 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 616 " 0.397 2.00e-02 2.50e+03 pdb="HD22 ASN C 616 " -0.391 2.00e-02 2.50e+03 ... (remaining 8623 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2141 2.16 - 2.77: 108907 2.77 - 3.38: 155481 3.38 - 3.99: 201870 3.99 - 4.60: 313662 Nonbonded interactions: 782061 Sorted by model distance: nonbonded pdb=" OE1 GLU B 661 " pdb=" H GLU B 661 " model vdw 1.551 1.850 nonbonded pdb=" OE1 GLU B 309 " pdb=" H GLU B 309 " model vdw 1.554 1.850 nonbonded pdb=" O ASP A 420 " pdb=" H LEU A 461 " model vdw 1.610 1.850 nonbonded pdb=" H LYS A 462 " pdb=" OE1 GLU A 465 " model vdw 1.613 1.850 nonbonded pdb=" H MET C 731 " pdb=" OE1 GLN C 774 " model vdw 1.614 1.850 ... (remaining 782056 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 15 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 123 through 656 or (resid 657 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name HA or name HB2 or name HB3)) or resid 658 through 1147)) selection = (chain 'B' and (resid 15 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 123 through 124 or (resid 125 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid \ 126 through 1147)) selection = (chain 'C' and (resid 15 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or resid 126 through 656 or (resid 65 \ 7 and (name N or name CA or name C or name O or name CB or name CG or name OD1 o \ r name ND2 or name HA or name HB2 or name HB3)) or resid 658 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 18039 2.51 5 N 4794 2.21 5 O 5457 1.98 5 H 27658 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 10.260 Check model and map are aligned: 0.800 Process input model: 131.460 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.390 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.003 0.038 29064 Z= 0.164 Angle : 0.499 5.548 39570 Z= 0.295 Chirality : 0.043 0.199 4488 Planarity : 0.003 0.059 5148 Dihedral : 10.432 88.228 10359 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.05 % Favored : 96.76 % 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: 0.26 (0.14), residues: 3642 helix: 2.03 (0.21), residues: 695 sheet: 0.41 (0.18), residues: 855 loop : -0.57 (0.13), residues: 2092 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 153 average time/residue: 0.8311 time to fit residues: 196.1958 Evaluate side-chains 132 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 3.299 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.6839 time to fit residues: 7.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 174 optimal weight: 0.0050 chunk 213 optimal weight: 2.9990 chunk 332 optimal weight: 20.0000 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A1005 GLN B 448 ASN B 532 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29064 Z= 0.227 Angle : 0.472 5.018 39570 Z= 0.253 Chirality : 0.042 0.164 4488 Planarity : 0.003 0.050 5148 Dihedral : 3.647 16.871 3945 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3642 helix: 1.91 (0.20), residues: 701 sheet: 0.08 (0.17), residues: 890 loop : -0.65 (0.13), residues: 2051 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 138 average time/residue: 0.8521 time to fit residues: 182.0931 Evaluate side-chains 130 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 3.279 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.6382 time to fit residues: 15.9202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 20.0000 chunk 359 optimal weight: 40.0000 chunk 296 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 40.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 29064 Z= 0.293 Angle : 0.487 5.491 39570 Z= 0.259 Chirality : 0.042 0.156 4488 Planarity : 0.003 0.046 5148 Dihedral : 3.766 16.188 3945 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer Outliers : 0.32 % 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: -0.18 (0.14), residues: 3642 helix: 1.68 (0.20), residues: 710 sheet: -0.10 (0.17), residues: 878 loop : -0.77 (0.13), residues: 2054 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.9188 time to fit residues: 184.0080 Evaluate side-chains 125 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 3.340 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.5974 time to fit residues: 12.7223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 30.0000 chunk 223 optimal weight: 4.9990 chunk 334 optimal weight: 0.9980 chunk 353 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 331 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 29064 Z= 0.290 Angle : 0.486 5.158 39570 Z= 0.259 Chirality : 0.042 0.144 4488 Planarity : 0.003 0.042 5148 Dihedral : 3.814 16.357 3945 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.74 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3642 helix: 1.65 (0.20), residues: 705 sheet: -0.18 (0.17), residues: 870 loop : -0.84 (0.13), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.8550 time to fit residues: 175.3081 Evaluate side-chains 128 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 3.311 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.5929 time to fit residues: 11.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 263 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 29064 Z= 0.219 Angle : 0.460 4.817 39570 Z= 0.244 Chirality : 0.042 0.147 4488 Planarity : 0.003 0.041 5148 Dihedral : 3.749 15.815 3945 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.29 % Rotamer Outliers : 0.22 % 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: -0.20 (0.14), residues: 3642 helix: 1.74 (0.20), residues: 705 sheet: -0.13 (0.17), residues: 858 loop : -0.80 (0.13), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 0.8670 time to fit residues: 176.6696 Evaluate side-chains 121 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 3.295 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.6861 time to fit residues: 8.7021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 6.9990 chunk 318 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 354 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 29064 Z= 0.219 Angle : 0.457 4.793 39570 Z= 0.242 Chirality : 0.042 0.145 4488 Planarity : 0.003 0.052 5148 Dihedral : 3.726 20.215 3945 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.10 % Rotamer Outliers : 0.29 % 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: -0.20 (0.14), residues: 3642 helix: 1.76 (0.20), residues: 706 sheet: -0.16 (0.17), residues: 866 loop : -0.79 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 129 average time/residue: 0.8477 time to fit residues: 170.9189 Evaluate side-chains 126 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 3.309 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6372 time to fit residues: 12.9544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 chunk 200 optimal weight: 1.9990 chunk 298 optimal weight: 0.0370 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 29064 Z= 0.250 Angle : 0.469 4.811 39570 Z= 0.248 Chirality : 0.042 0.174 4488 Planarity : 0.003 0.050 5148 Dihedral : 3.739 17.474 3945 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer Outliers : 0.25 % 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: -0.25 (0.14), residues: 3642 helix: 1.72 (0.20), residues: 707 sheet: -0.18 (0.17), residues: 866 loop : -0.82 (0.13), residues: 2069 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.8510 time to fit residues: 168.3757 Evaluate side-chains 121 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 3.306 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.6551 time to fit residues: 11.8423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 29064 Z= 0.170 Angle : 0.449 4.694 39570 Z= 0.237 Chirality : 0.042 0.149 4488 Planarity : 0.003 0.054 5148 Dihedral : 3.671 17.576 3945 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer Outliers : 0.13 % 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: -0.15 (0.14), residues: 3642 helix: 1.87 (0.20), residues: 700 sheet: -0.16 (0.17), residues: 869 loop : -0.76 (0.13), residues: 2073 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 122 average time/residue: 0.8846 time to fit residues: 170.5723 Evaluate side-chains 118 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 3.400 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.8597 time to fit residues: 9.9895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.5980 chunk 337 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29064 Z= 0.220 Angle : 0.459 4.774 39570 Z= 0.242 Chirality : 0.041 0.143 4488 Planarity : 0.003 0.053 5148 Dihedral : 3.663 16.120 3945 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.74 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3642 helix: 1.86 (0.20), residues: 701 sheet: -0.19 (0.17), residues: 878 loop : -0.78 (0.13), residues: 2063 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 120 average time/residue: 0.8427 time to fit residues: 159.0266 Evaluate side-chains 118 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 3.282 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.6816 time to fit residues: 10.9824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.6980 chunk 347 optimal weight: 30.0000 chunk 212 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 241 optimal weight: 0.4980 chunk 364 optimal weight: 9.9990 chunk 335 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 224 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 29064 Z= 0.135 Angle : 0.444 6.493 39570 Z= 0.233 Chirality : 0.042 0.152 4488 Planarity : 0.003 0.052 5148 Dihedral : 3.612 16.928 3945 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer Outliers : 0.13 % 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 (0.14), residues: 3642 helix: 1.99 (0.20), residues: 700 sheet: -0.10 (0.17), residues: 864 loop : -0.70 (0.13), residues: 2078 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 116 average time/residue: 0.8689 time to fit residues: 158.6867 Evaluate side-chains 117 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 3.293 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.6869 time to fit residues: 8.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.113508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063444 restraints weight = 265474.792| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.39 r_work: 0.3040 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 29064 Z= 0.260 Angle : 0.467 4.859 39570 Z= 0.246 Chirality : 0.042 0.141 4488 Planarity : 0.003 0.052 5148 Dihedral : 3.658 15.811 3945 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer Outliers : 0.13 % 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: -0.15 (0.14), residues: 3642 helix: 1.86 (0.20), residues: 713 sheet: -0.16 (0.17), residues: 867 loop : -0.77 (0.13), residues: 2062 =============================================================================== Job complete usr+sys time: 7801.94 seconds wall clock time: 137 minutes 15.08 seconds (8235.08 seconds total)