Starting phenix.real_space_refine on Fri Mar 6 14:03:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lla_23413/03_2026/7lla_23413.map" } resolution = 2.97 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 20380 2.51 5 N 5388 2.21 5 O 5940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'ACO': 1, 'OAA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.46, per 1000 atoms: 0.42 Number of scatterers: 31900 At special positions: 0 Unit cell: (162.69, 140.07, 171.39, 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 180 16.00 P 12 15.00 O 5940 8.00 N 5388 7.00 C 20380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 36 sheets defined 45.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.520A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.071A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.659A pdb=" N LYS A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.600A pdb=" N GLY A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 removed outlier: 3.884A pdb=" N ALA A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.715A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.729A pdb=" N LEU A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.562A pdb=" N SER A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 664 through 678 removed outlier: 4.231A pdb=" N ASN A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.672A pdb=" N HIS A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 733 Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 792 through 806 removed outlier: 3.654A pdb=" N ALA A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 878 Processing helix chain 'A' and resid 883 through 896 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 952 Processing helix chain 'A' and resid 955 through 966 removed outlier: 3.575A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.571A pdb=" N ASP A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.797A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1055 removed outlier: 4.460A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 4.064A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 3.836A pdb=" N ILE A1091 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.520A pdb=" N HIS B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.071A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.659A pdb=" N LYS B 177 " --> pdb=" O PRO B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.599A pdb=" N GLY B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.883A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 312 through 325 Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.715A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.729A pdb=" N LEU B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.561A pdb=" N SER B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 664 through 678 removed outlier: 4.232A pdb=" N ASN B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.672A pdb=" N HIS B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 733 Processing helix chain 'B' and resid 767 through 770 Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 792 through 806 removed outlier: 3.653A pdb=" N ALA B 806 " --> pdb=" O GLU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 878 Processing helix chain 'B' and resid 883 through 896 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 952 Processing helix chain 'B' and resid 955 through 966 removed outlier: 3.575A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 998 Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.571A pdb=" N ASP B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 3.796A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1055 removed outlier: 4.461A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1079 removed outlier: 4.064A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 removed outlier: 3.836A pdb=" N ILE B1091 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.520A pdb=" N HIS C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.071A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 174 through 177 removed outlier: 3.659A pdb=" N LYS C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 178 through 195 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.601A pdb=" N GLY C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.883A pdb=" N ALA C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 312 through 325 Processing helix chain 'C' and resid 349 through 364 removed outlier: 3.715A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.729A pdb=" N LEU C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 556 through 563 Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.651A pdb=" N SER C 581 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 664 through 678 removed outlier: 4.231A pdb=" N ASN C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 707 removed outlier: 3.671A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 Processing helix chain 'C' and resid 767 through 770 Processing helix chain 'C' and resid 771 through 781 Processing helix chain 'C' and resid 792 through 806 removed outlier: 3.653A pdb=" N ALA C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 878 Processing helix chain 'C' and resid 883 through 896 Processing helix chain 'C' and resid 904 through 916 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 937 through 952 Processing helix chain 'C' and resid 955 through 966 removed outlier: 3.575A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 998 Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.571A pdb=" N ASP C1005 " --> pdb=" O THR C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 3.797A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1055 removed outlier: 4.461A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C1053 " --> pdb=" O ASP C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 4.063A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.836A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.520A pdb=" N HIS D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.072A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 174 through 177 removed outlier: 3.659A pdb=" N LYS D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 177' Processing helix chain 'D' and resid 178 through 195 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 229 through 234 removed outlier: 3.599A pdb=" N GLY D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 removed outlier: 3.883A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 312 through 325 Processing helix chain 'D' and resid 349 through 364 removed outlier: 3.714A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.729A pdb=" N LEU D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.560A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 664 through 678 removed outlier: 4.231A pdb=" N ASN D 668 " --> pdb=" O GLY D 664 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.672A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 767 through 770 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 792 through 806 removed outlier: 3.653A pdb=" N ALA D 806 " --> pdb=" O GLU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 831 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 878 Processing helix chain 'D' and resid 883 through 896 Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 Processing helix chain 'D' and resid 937 through 952 Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.575A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 998 Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.571A pdb=" N ASP D1005 " --> pdb=" O THR D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 3.797A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1055 removed outlier: 4.460A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D1053 " --> pdb=" O ASP D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1079 removed outlier: 4.063A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.837A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.775A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA A 218 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 200 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 220 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 4.345A pdb=" N ASN A 54 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 55 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 75 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 280 removed outlier: 3.507A pdb=" N ILE A 339 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.202A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 594 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 634 through 635 removed outlier: 7.291A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 716 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 660 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP A 743 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 715 " --> pdb=" O TRP A 743 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 823 through 824 removed outlier: 6.220A pdb=" N MET A 823 " --> pdb=" O ARG B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 34 removed outlier: 4.344A pdb=" N ASN B 54 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 55 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 75 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB5, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AB6, first strand: chain 'B' and resid 263 through 268 Processing sheet with id=AB7, first strand: chain 'B' and resid 275 through 280 removed outlier: 3.507A pdb=" N ILE B 339 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 537 through 543 removed outlier: 7.202A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 594 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 634 through 635 removed outlier: 7.292A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE B 713 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP B 743 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 715 " --> pdb=" O TRP B 743 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA C 219 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 218 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 200 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 220 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.346A pdb=" N ASN C 54 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 55 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 75 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC4, first strand: chain 'C' and resid 205 through 207 Processing sheet with id=AC5, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AC6, first strand: chain 'C' and resid 275 through 280 removed outlier: 3.507A pdb=" N ILE C 339 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.203A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 594 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 634 through 635 removed outlier: 7.292A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP C 743 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 715 " --> pdb=" O TRP C 743 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.201A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 32 through 34 removed outlier: 4.345A pdb=" N ASN D 54 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 55 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D 75 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD5, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AD6, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AD7, first strand: chain 'D' and resid 275 through 280 removed outlier: 3.506A pdb=" N ILE D 339 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.203A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 594 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 634 through 635 removed outlier: 7.292A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 4086 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: 7.55 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5308 1.30 - 1.43: 8074 1.43 - 1.56: 18899 1.56 - 1.69: 19 1.69 - 1.81: 292 Bond restraints: 32592 Sorted by residual: bond pdb=" C5A ACO B1201 " pdb=" N7A ACO B1201 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C5A ACO D1202 " pdb=" N7A ACO D1202 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.20e+01 bond pdb=" C5A ACO C1202 " pdb=" N7A ACO C1202 " ideal model delta sigma weight residual 1.387 1.310 0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C8A ACO D1202 " pdb=" N9A ACO D1202 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.00e-02 1.00e+04 3.69e+01 ... (remaining 32587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 43758 3.95 - 7.91: 334 7.91 - 11.86: 60 11.86 - 15.82: 0 15.82 - 19.77: 4 Bond angle restraints: 44156 Sorted by residual: angle pdb=" P1A ACO B1201 " pdb=" O3A ACO B1201 " pdb=" P2A ACO B1201 " ideal model delta sigma weight residual 136.83 125.86 10.97 1.00e+00 1.00e+00 1.20e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 126.03 10.80 1.00e+00 1.00e+00 1.17e+02 angle pdb=" P1A ACO D1202 " pdb=" O3A ACO D1202 " pdb=" P2A ACO D1202 " ideal model delta sigma weight residual 136.83 126.13 10.70 1.00e+00 1.00e+00 1.14e+02 angle pdb=" P1A ACO C1202 " pdb=" O3A ACO C1202 " pdb=" P2A ACO C1202 " ideal model delta sigma weight residual 136.83 126.20 10.63 1.00e+00 1.00e+00 1.13e+02 angle pdb=" O3B ACO A1201 " pdb=" P3B ACO A1201 " pdb=" O7A ACO A1201 " ideal model delta sigma weight residual 107.97 99.62 8.35 1.00e+00 1.00e+00 6.98e+01 ... (remaining 44151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.78: 17984 20.78 - 41.56: 1306 41.56 - 62.35: 206 62.35 - 83.13: 44 83.13 - 103.91: 12 Dihedral angle restraints: 19552 sinusoidal: 7912 harmonic: 11640 Sorted by residual: dihedral pdb=" CA ARG B1045 " pdb=" C ARG B1045 " pdb=" N GLU B1046 " pdb=" CA GLU B1046 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG A1045 " pdb=" C ARG A1045 " pdb=" N GLU A1046 " pdb=" CA GLU A1046 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG D1045 " pdb=" C ARG D1045 " pdb=" N GLU D1046 " pdb=" CA GLU D1046 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3849 0.064 - 0.128: 911 0.128 - 0.192: 112 0.192 - 0.256: 36 0.256 - 0.320: 4 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CB ILE C 123 " pdb=" CA ILE C 123 " pdb=" CG1 ILE C 123 " pdb=" CG2 ILE C 123 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE D 123 " pdb=" CA ILE D 123 " pdb=" CG1 ILE D 123 " pdb=" CG2 ILE D 123 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4909 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1202 " -0.193 2.00e-02 2.50e+03 1.56e-01 3.03e+02 pdb=" C9P ACO D1202 " 0.075 2.00e-02 2.50e+03 pdb=" CAP ACO D1202 " -0.148 2.00e-02 2.50e+03 pdb=" N8P ACO D1202 " 0.236 2.00e-02 2.50e+03 pdb=" O9P ACO D1202 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C1202 " 0.189 2.00e-02 2.50e+03 1.52e-01 2.90e+02 pdb=" C9P ACO C1202 " -0.074 2.00e-02 2.50e+03 pdb=" CAP ACO C1202 " 0.145 2.00e-02 2.50e+03 pdb=" N8P ACO C1202 " -0.231 2.00e-02 2.50e+03 pdb=" O9P ACO C1202 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO B1201 " -0.189 2.00e-02 2.50e+03 1.52e-01 2.90e+02 pdb=" C9P ACO B1201 " 0.073 2.00e-02 2.50e+03 pdb=" CAP ACO B1201 " -0.145 2.00e-02 2.50e+03 pdb=" N8P ACO B1201 " 0.230 2.00e-02 2.50e+03 pdb=" O9P ACO B1201 " 0.031 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7263 2.79 - 3.32: 27925 3.32 - 3.84: 53956 3.84 - 4.37: 62158 4.37 - 4.90: 109214 Nonbonded interactions: 260516 Sorted by model distance: nonbonded pdb=" O ASN D 671 " pdb=" OG SER D 675 " model vdw 2.260 3.040 nonbonded pdb=" O ASN B 671 " pdb=" OG SER B 675 " model vdw 2.260 3.040 nonbonded pdb=" O ASN A 671 " pdb=" OG SER A 675 " model vdw 2.260 3.040 nonbonded pdb=" O ASN C 671 " pdb=" OG SER C 675 " model vdw 2.260 3.040 nonbonded pdb=" O LYS A 265 " pdb=" OH TYR A 319 " model vdw 2.289 3.040 ... (remaining 260511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.830 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 32592 Z= 0.356 Angle : 0.958 19.773 44156 Z= 0.556 Chirality : 0.057 0.320 4912 Planarity : 0.008 0.156 5652 Dihedral : 14.873 103.910 12160 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.59 % Allowed : 0.89 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.11), residues: 4068 helix: -1.73 (0.10), residues: 1708 sheet: -0.18 (0.22), residues: 588 loop : -1.79 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1078 TYR 0.017 0.002 TYR A 124 PHE 0.018 0.002 PHE A 197 TRP 0.014 0.001 TRP B 743 HIS 0.006 0.001 HIS A 997 Details of bonding type rmsd covalent geometry : bond 0.00570 (32592) covalent geometry : angle 0.95828 (44156) hydrogen bonds : bond 0.15048 ( 1418) hydrogen bonds : angle 7.30747 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 367 time to evaluate : 1.199 Fit side-chains REVERT: B 614 ASP cc_start: 0.7531 (m-30) cc_final: 0.7309 (m-30) REVERT: C 491 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (t) REVERT: D 496 HIS cc_start: 0.7535 (m-70) cc_final: 0.7321 (m90) outliers start: 20 outliers final: 11 residues processed: 379 average time/residue: 0.6993 time to fit residues: 312.1669 Evaluate side-chains 273 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 40.0000 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.211489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137586 restraints weight = 69630.655| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.03 r_work: 0.3375 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32592 Z= 0.123 Angle : 0.594 10.427 44156 Z= 0.306 Chirality : 0.045 0.153 4912 Planarity : 0.005 0.060 5652 Dihedral : 8.344 99.837 4683 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.07 % Allowed : 8.46 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4068 helix: -0.36 (0.12), residues: 1768 sheet: -0.16 (0.23), residues: 588 loop : -1.54 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 703 TYR 0.014 0.001 TYR D 199 PHE 0.015 0.001 PHE D 191 TRP 0.012 0.001 TRP D 233 HIS 0.002 0.000 HIS D 563 Details of bonding type rmsd covalent geometry : bond 0.00275 (32592) covalent geometry : angle 0.59406 (44156) hydrogen bonds : bond 0.03704 ( 1418) hydrogen bonds : angle 5.01571 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 1.203 Fit side-chains REVERT: A 364 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5875 (t80) REVERT: A 491 THR cc_start: 0.8381 (m) cc_final: 0.8095 (t) REVERT: B 614 ASP cc_start: 0.7766 (m-30) cc_final: 0.7419 (m-30) REVERT: C 1035 ASP cc_start: 0.7658 (t0) cc_final: 0.7418 (t0) REVERT: D 1035 ASP cc_start: 0.7408 (t0) cc_final: 0.7172 (t0) outliers start: 36 outliers final: 9 residues processed: 288 average time/residue: 0.6053 time to fit residues: 210.7065 Evaluate side-chains 263 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 253 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 545 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 181 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 377 optimal weight: 0.1980 chunk 172 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 997 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.206922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131948 restraints weight = 69236.052| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.86 r_work: 0.3266 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32592 Z= 0.156 Angle : 0.594 9.980 44156 Z= 0.304 Chirality : 0.046 0.227 4912 Planarity : 0.005 0.052 5652 Dihedral : 7.667 90.142 4664 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.22 % Allowed : 9.62 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 4068 helix: 0.18 (0.12), residues: 1764 sheet: -0.44 (0.23), residues: 560 loop : -1.30 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 703 TYR 0.027 0.002 TYR B 16 PHE 0.015 0.001 PHE A 697 TRP 0.008 0.001 TRP B 233 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00374 (32592) covalent geometry : angle 0.59400 (44156) hydrogen bonds : bond 0.03621 ( 1418) hydrogen bonds : angle 4.61181 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5818 (t80) REVERT: A 491 THR cc_start: 0.8633 (m) cc_final: 0.8393 (t) REVERT: A 971 MET cc_start: 0.8637 (ttm) cc_final: 0.8344 (ttt) REVERT: A 992 ASP cc_start: 0.7723 (m-30) cc_final: 0.7242 (m-30) REVERT: A 1035 ASP cc_start: 0.8006 (t0) cc_final: 0.7766 (t0) REVERT: B 614 ASP cc_start: 0.7869 (m-30) cc_final: 0.7513 (m-30) REVERT: C 698 MET cc_start: 0.7280 (mmm) cc_final: 0.6248 (mmm) REVERT: C 992 ASP cc_start: 0.7857 (m-30) cc_final: 0.7307 (m-30) REVERT: C 1035 ASP cc_start: 0.7824 (t0) cc_final: 0.7595 (t0) REVERT: D 196 TYR cc_start: 0.6110 (m-80) cc_final: 0.5361 (m-10) REVERT: D 197 PHE cc_start: 0.8030 (m-10) cc_final: 0.7722 (m-10) REVERT: D 379 ARG cc_start: 0.6660 (mmm160) cc_final: 0.6424 (mmm160) REVERT: D 545 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6843 (p-80) REVERT: D 733 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7399 (mt-10) REVERT: D 971 MET cc_start: 0.8577 (ttm) cc_final: 0.8353 (ttt) REVERT: D 1035 ASP cc_start: 0.7704 (t0) cc_final: 0.7461 (t0) outliers start: 41 outliers final: 17 residues processed: 288 average time/residue: 0.6513 time to fit residues: 224.6662 Evaluate side-chains 265 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 68 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 170 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 chunk 192 optimal weight: 0.0770 chunk 138 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1024 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.199941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113649 restraints weight = 64230.723| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.25 r_work: 0.3215 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32592 Z= 0.169 Angle : 0.596 12.065 44156 Z= 0.302 Chirality : 0.046 0.358 4912 Planarity : 0.004 0.048 5652 Dihedral : 7.352 84.713 4660 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.31 % Allowed : 11.07 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4068 helix: 0.30 (0.12), residues: 1776 sheet: -0.43 (0.23), residues: 560 loop : -1.27 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1085 TYR 0.015 0.002 TYR B 692 PHE 0.017 0.001 PHE D 354 TRP 0.005 0.001 TRP D 233 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00414 (32592) covalent geometry : angle 0.59626 (44156) hydrogen bonds : bond 0.03544 ( 1418) hydrogen bonds : angle 4.53837 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5772 (t80) REVERT: A 376 PHE cc_start: 0.4698 (m-80) cc_final: 0.4466 (m-10) REVERT: A 491 THR cc_start: 0.8496 (m) cc_final: 0.8250 (t) REVERT: A 545 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6657 (p-80) REVERT: A 971 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8173 (ttt) REVERT: A 1035 ASP cc_start: 0.7364 (t0) cc_final: 0.7115 (t0) REVERT: B 391 MET cc_start: 0.5936 (mmm) cc_final: 0.5698 (mmm) REVERT: B 614 ASP cc_start: 0.7678 (m-30) cc_final: 0.7345 (m-30) REVERT: B 777 GLN cc_start: 0.7600 (pp30) cc_final: 0.7291 (pt0) REVERT: C 545 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6720 (p-80) REVERT: C 777 GLN cc_start: 0.7550 (pp30) cc_final: 0.7201 (pt0) REVERT: C 971 MET cc_start: 0.8438 (ttm) cc_final: 0.8053 (ttt) REVERT: C 1035 ASP cc_start: 0.7185 (t0) cc_final: 0.6932 (t0) REVERT: D 196 TYR cc_start: 0.5980 (m-80) cc_final: 0.5436 (m-10) REVERT: D 197 PHE cc_start: 0.7309 (m-10) cc_final: 0.6973 (m-10) REVERT: D 777 GLN cc_start: 0.7492 (pp30) cc_final: 0.7091 (pt0) REVERT: D 971 MET cc_start: 0.8395 (ttm) cc_final: 0.8104 (ttt) REVERT: D 1035 ASP cc_start: 0.7189 (t0) cc_final: 0.6932 (t0) outliers start: 44 outliers final: 22 residues processed: 275 average time/residue: 0.6321 time to fit residues: 208.5034 Evaluate side-chains 263 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 251 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 362 optimal weight: 0.4980 chunk 224 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 380 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN D 879 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.202620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122852 restraints weight = 68607.811| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.56 r_work: 0.3197 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32592 Z= 0.111 Angle : 0.551 12.830 44156 Z= 0.279 Chirality : 0.044 0.333 4912 Planarity : 0.004 0.044 5652 Dihedral : 6.968 76.955 4660 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.16 % Allowed : 11.70 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4068 helix: 0.54 (0.13), residues: 1780 sheet: -0.34 (0.24), residues: 560 loop : -1.21 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1085 TYR 0.028 0.001 TYR B 16 PHE 0.015 0.001 PHE B 354 TRP 0.005 0.001 TRP B 233 HIS 0.002 0.000 HIS C 975 Details of bonding type rmsd covalent geometry : bond 0.00260 (32592) covalent geometry : angle 0.55118 (44156) hydrogen bonds : bond 0.03170 ( 1418) hydrogen bonds : angle 4.34276 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5739 (t80) REVERT: A 376 PHE cc_start: 0.4760 (m-80) cc_final: 0.4539 (m-10) REVERT: A 491 THR cc_start: 0.8463 (m) cc_final: 0.8248 (t) REVERT: A 545 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6736 (p-80) REVERT: A 971 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8173 (ttt) REVERT: A 1035 ASP cc_start: 0.7341 (t0) cc_final: 0.7067 (t0) REVERT: B 545 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6691 (p-80) REVERT: B 698 MET cc_start: 0.6306 (mmm) cc_final: 0.5295 (mmm) REVERT: B 732 LYS cc_start: 0.7367 (mtmm) cc_final: 0.7143 (mmpt) REVERT: B 777 GLN cc_start: 0.7471 (pp30) cc_final: 0.7209 (pt0) REVERT: B 881 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8129 (mtp180) REVERT: B 971 MET cc_start: 0.8396 (ttm) cc_final: 0.8006 (ttt) REVERT: B 1024 ASN cc_start: 0.8106 (m110) cc_final: 0.7722 (p0) REVERT: C 545 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6697 (p-80) REVERT: C 971 MET cc_start: 0.8448 (ttm) cc_final: 0.8071 (ttt) REVERT: C 977 VAL cc_start: 0.8178 (m) cc_final: 0.7957 (p) REVERT: C 1035 ASP cc_start: 0.7201 (t0) cc_final: 0.6934 (t0) REVERT: D 698 MET cc_start: 0.6436 (mmm) cc_final: 0.5437 (mmm) REVERT: D 732 LYS cc_start: 0.7256 (mtmm) cc_final: 0.7005 (mmpt) REVERT: D 777 GLN cc_start: 0.7493 (pp30) cc_final: 0.7290 (pp30) REVERT: D 971 MET cc_start: 0.8471 (ttm) cc_final: 0.8132 (ttt) REVERT: D 1035 ASP cc_start: 0.7158 (t0) cc_final: 0.6895 (t0) outliers start: 39 outliers final: 17 residues processed: 281 average time/residue: 0.6682 time to fit residues: 224.1138 Evaluate side-chains 255 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 79 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 351 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** 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 = 0.4363 r_free = 0.4363 target = 0.197913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110833 restraints weight = 60308.446| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.07 r_work: 0.3201 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32592 Z= 0.193 Angle : 0.628 13.675 44156 Z= 0.316 Chirality : 0.048 0.433 4912 Planarity : 0.004 0.042 5652 Dihedral : 7.097 75.232 4660 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.19 % Allowed : 11.85 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4068 helix: 0.47 (0.12), residues: 1776 sheet: -0.42 (0.24), residues: 560 loop : -1.22 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 703 TYR 0.016 0.002 TYR D 885 PHE 0.018 0.002 PHE D 354 TRP 0.006 0.001 TRP D 233 HIS 0.005 0.001 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00473 (32592) covalent geometry : angle 0.62797 (44156) hydrogen bonds : bond 0.03663 ( 1418) hydrogen bonds : angle 4.49048 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5667 (ttt90) REVERT: A 122 CYS cc_start: 0.7203 (t) cc_final: 0.6892 (t) REVERT: A 364 TYR cc_start: 0.6158 (OUTLIER) cc_final: 0.5758 (t80) REVERT: A 491 THR cc_start: 0.8545 (m) cc_final: 0.8334 (t) REVERT: A 777 GLN cc_start: 0.7676 (pp30) cc_final: 0.7356 (pt0) REVERT: A 971 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (ttt) REVERT: B 196 TYR cc_start: 0.6368 (m-80) cc_final: 0.5878 (m-10) REVERT: B 545 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6974 (p-80) REVERT: B 732 LYS cc_start: 0.7353 (mtmm) cc_final: 0.7130 (mmpt) REVERT: B 777 GLN cc_start: 0.7541 (pp30) cc_final: 0.7261 (pt0) REVERT: B 971 MET cc_start: 0.8487 (ttm) cc_final: 0.8140 (ttt) REVERT: C 197 PHE cc_start: 0.7569 (m-10) cc_final: 0.7253 (m-10) REVERT: C 545 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6909 (p-80) REVERT: C 971 MET cc_start: 0.8560 (ttm) cc_final: 0.8227 (ttt) REVERT: C 1035 ASP cc_start: 0.7355 (t0) cc_final: 0.7099 (t0) REVERT: D 732 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6984 (mmpt) REVERT: D 971 MET cc_start: 0.8528 (ttm) cc_final: 0.8228 (ttt) REVERT: D 1035 ASP cc_start: 0.7328 (t0) cc_final: 0.7063 (t0) outliers start: 40 outliers final: 25 residues processed: 255 average time/residue: 0.6557 time to fit residues: 200.1516 Evaluate side-chains 255 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 796 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 1036 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 258 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 284 optimal weight: 0.0050 chunk 185 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 266 optimal weight: 0.0670 chunk 351 optimal weight: 0.7980 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN A 879 GLN ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117758 restraints weight = 57749.010| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.13 r_work: 0.3293 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32592 Z= 0.102 Angle : 0.558 11.970 44156 Z= 0.280 Chirality : 0.045 0.369 4912 Planarity : 0.004 0.040 5652 Dihedral : 6.666 68.881 4660 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.07 % Allowed : 12.32 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4068 helix: 0.75 (0.13), residues: 1768 sheet: -0.29 (0.24), residues: 560 loop : -1.13 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 703 TYR 0.024 0.001 TYR B 16 PHE 0.014 0.001 PHE A 354 TRP 0.006 0.001 TRP D 233 HIS 0.002 0.000 HIS D1072 Details of bonding type rmsd covalent geometry : bond 0.00229 (32592) covalent geometry : angle 0.55814 (44156) hydrogen bonds : bond 0.03045 ( 1418) hydrogen bonds : angle 4.26603 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5616 (mtp85) REVERT: A 364 TYR cc_start: 0.6157 (OUTLIER) cc_final: 0.5767 (t80) REVERT: A 971 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8094 (ttt) REVERT: B 376 PHE cc_start: 0.4696 (m-80) cc_final: 0.4490 (m-10) REVERT: B 545 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6813 (p-80) REVERT: B 732 LYS cc_start: 0.7371 (mtmm) cc_final: 0.7153 (mmpt) REVERT: B 777 GLN cc_start: 0.7555 (pp30) cc_final: 0.7296 (pt0) REVERT: B 881 ARG cc_start: 0.8259 (ttp80) cc_final: 0.8042 (mtp180) REVERT: B 971 MET cc_start: 0.8358 (ttm) cc_final: 0.7984 (ttt) REVERT: B 1024 ASN cc_start: 0.7955 (m110) cc_final: 0.7734 (p0) REVERT: B 1035 ASP cc_start: 0.7302 (t0) cc_final: 0.7007 (t0) REVERT: C 197 PHE cc_start: 0.7180 (m-10) cc_final: 0.6929 (m-10) REVERT: C 545 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6692 (p-80) REVERT: C 971 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8070 (ttt) REVERT: C 1035 ASP cc_start: 0.7044 (t0) cc_final: 0.6785 (t0) REVERT: D 732 LYS cc_start: 0.7253 (mtmm) cc_final: 0.6966 (mmpt) REVERT: D 777 GLN cc_start: 0.7264 (pp30) cc_final: 0.6951 (pt0) REVERT: D 881 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7909 (mtp180) REVERT: D 965 LYS cc_start: 0.8236 (mttp) cc_final: 0.7974 (pttp) REVERT: D 971 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8142 (ttt) REVERT: D 1035 ASP cc_start: 0.7041 (t0) cc_final: 0.6784 (t0) outliers start: 36 outliers final: 16 residues processed: 261 average time/residue: 0.6925 time to fit residues: 214.4583 Evaluate side-chains 253 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 971 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 364 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** 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 = 0.4396 r_free = 0.4396 target = 0.201204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124393 restraints weight = 79807.460| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.76 r_work: 0.3171 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32592 Z= 0.126 Angle : 0.572 13.694 44156 Z= 0.286 Chirality : 0.045 0.440 4912 Planarity : 0.004 0.039 5652 Dihedral : 6.574 69.489 4660 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.04 % Allowed : 12.95 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4068 helix: 0.78 (0.12), residues: 1776 sheet: -0.28 (0.24), residues: 568 loop : -1.08 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1085 TYR 0.013 0.001 TYR A 124 PHE 0.016 0.001 PHE A 354 TRP 0.007 0.001 TRP A 276 HIS 0.002 0.000 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00300 (32592) covalent geometry : angle 0.57230 (44156) hydrogen bonds : bond 0.03127 ( 1418) hydrogen bonds : angle 4.23524 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5611 (mtp85) REVERT: A 364 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5765 (t80) REVERT: A 777 GLN cc_start: 0.7738 (pp30) cc_final: 0.7440 (pt0) REVERT: A 971 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (ttt) REVERT: B 376 PHE cc_start: 0.4751 (m-80) cc_final: 0.4546 (m-10) REVERT: B 614 ASP cc_start: 0.7893 (m-30) cc_final: 0.7589 (m-30) REVERT: B 732 LYS cc_start: 0.7454 (mtmm) cc_final: 0.7213 (mmpt) REVERT: B 777 GLN cc_start: 0.7588 (pp30) cc_final: 0.7342 (pt0) REVERT: B 971 MET cc_start: 0.8480 (ttm) cc_final: 0.8133 (ttt) REVERT: B 1024 ASN cc_start: 0.8202 (m110) cc_final: 0.7887 (p0) REVERT: C 197 PHE cc_start: 0.7205 (m-10) cc_final: 0.6988 (m-10) REVERT: C 545 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6915 (p-80) REVERT: C 732 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7281 (mmpt) REVERT: C 777 GLN cc_start: 0.7836 (pp30) cc_final: 0.7353 (pt0) REVERT: C 881 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8099 (mtp180) REVERT: C 971 MET cc_start: 0.8588 (ttm) cc_final: 0.8213 (ttt) REVERT: C 1035 ASP cc_start: 0.7336 (t0) cc_final: 0.7052 (t0) REVERT: D 614 ASP cc_start: 0.7855 (m-30) cc_final: 0.7514 (m-30) REVERT: D 732 LYS cc_start: 0.7327 (mtmm) cc_final: 0.7015 (mmpt) REVERT: D 777 GLN cc_start: 0.7346 (pp30) cc_final: 0.7059 (pt0) REVERT: D 881 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8063 (mtp180) REVERT: D 965 LYS cc_start: 0.8306 (mttp) cc_final: 0.8030 (pttp) REVERT: D 971 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8236 (ttt) REVERT: D 1035 ASP cc_start: 0.7300 (t0) cc_final: 0.7027 (t0) outliers start: 35 outliers final: 21 residues processed: 256 average time/residue: 0.6850 time to fit residues: 209.6125 Evaluate side-chains 256 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 971 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 313 optimal weight: 0.0670 chunk 248 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 336 optimal weight: 40.0000 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 356 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 overall best weight: 3.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.197325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110295 restraints weight = 65310.813| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.15 r_work: 0.3194 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32592 Z= 0.195 Angle : 0.641 17.526 44156 Z= 0.319 Chirality : 0.048 0.506 4912 Planarity : 0.004 0.040 5652 Dihedral : 6.840 68.952 4660 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.95 % Allowed : 13.21 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4068 helix: 0.60 (0.12), residues: 1776 sheet: -0.30 (0.24), residues: 560 loop : -1.14 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 703 TYR 0.026 0.002 TYR B 16 PHE 0.020 0.002 PHE B 354 TRP 0.008 0.001 TRP B 276 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00474 (32592) covalent geometry : angle 0.64141 (44156) hydrogen bonds : bond 0.03630 ( 1418) hydrogen bonds : angle 4.42246 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5662 (ttt90) REVERT: A 122 CYS cc_start: 0.7160 (t) cc_final: 0.6866 (t) REVERT: A 364 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5814 (t80) REVERT: A 777 GLN cc_start: 0.7673 (pp30) cc_final: 0.7379 (pt0) REVERT: A 971 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (ttt) REVERT: A 1045 ARG cc_start: 0.7687 (tpt170) cc_final: 0.7422 (mmm160) REVERT: B 732 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7122 (mmpt) REVERT: B 777 GLN cc_start: 0.7532 (pp30) cc_final: 0.7236 (pt0) REVERT: B 971 MET cc_start: 0.8499 (ttm) cc_final: 0.8177 (ttt) REVERT: B 1035 ASP cc_start: 0.7573 (t0) cc_final: 0.7359 (t0) REVERT: B 1045 ARG cc_start: 0.7690 (tpt170) cc_final: 0.7420 (mmm160) REVERT: C 732 LYS cc_start: 0.7430 (mtmm) cc_final: 0.7128 (mmtm) REVERT: C 777 GLN cc_start: 0.7820 (pp30) cc_final: 0.7368 (pt0) REVERT: C 971 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8248 (ttt) REVERT: C 1035 ASP cc_start: 0.7341 (t0) cc_final: 0.7073 (t0) REVERT: D 777 GLN cc_start: 0.7374 (pp30) cc_final: 0.7045 (pt0) REVERT: D 971 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8293 (ttt) REVERT: D 1035 ASP cc_start: 0.7302 (t0) cc_final: 0.7052 (t0) outliers start: 32 outliers final: 21 residues processed: 253 average time/residue: 0.6666 time to fit residues: 201.3029 Evaluate side-chains 253 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 971 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 392 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 326 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 300 optimal weight: 0.9980 chunk 359 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 345 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** 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 = 0.4393 r_free = 0.4393 target = 0.202180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123218 restraints weight = 76194.893| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.85 r_work: 0.3183 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32592 Z= 0.132 Angle : 0.601 16.960 44156 Z= 0.297 Chirality : 0.046 0.514 4912 Planarity : 0.004 0.040 5652 Dihedral : 6.654 68.534 4660 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.80 % Allowed : 13.45 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4068 helix: 0.74 (0.12), residues: 1768 sheet: -0.51 (0.24), residues: 536 loop : -1.04 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1085 TYR 0.014 0.001 TYR A 124 PHE 0.017 0.001 PHE B 354 TRP 0.008 0.001 TRP B 276 HIS 0.002 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00316 (32592) covalent geometry : angle 0.60148 (44156) hydrogen bonds : bond 0.03276 ( 1418) hydrogen bonds : angle 4.31360 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.5625 (mtp85) REVERT: A 122 CYS cc_start: 0.7279 (t) cc_final: 0.6992 (t) REVERT: A 364 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 777 GLN cc_start: 0.7702 (pp30) cc_final: 0.7433 (pt0) REVERT: A 971 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (ttt) REVERT: B 732 LYS cc_start: 0.7401 (mtmm) cc_final: 0.7185 (mmpt) REVERT: B 777 GLN cc_start: 0.7579 (pp30) cc_final: 0.7315 (pt0) REVERT: B 971 MET cc_start: 0.8491 (ttm) cc_final: 0.8150 (ttt) REVERT: C 197 PHE cc_start: 0.7494 (m-10) cc_final: 0.7263 (m-10) REVERT: C 732 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7263 (mmtm) REVERT: C 777 GLN cc_start: 0.7842 (pp30) cc_final: 0.7444 (pt0) REVERT: C 971 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8227 (ttt) REVERT: C 1035 ASP cc_start: 0.7285 (t0) cc_final: 0.7017 (t0) REVERT: D 391 MET cc_start: 0.5752 (mmm) cc_final: 0.5547 (mmm) REVERT: D 614 ASP cc_start: 0.7893 (m-30) cc_final: 0.7537 (m-30) REVERT: D 732 LYS cc_start: 0.7333 (mtmm) cc_final: 0.7029 (mmpt) REVERT: D 777 GLN cc_start: 0.7391 (pp30) cc_final: 0.7019 (pm20) REVERT: D 965 LYS cc_start: 0.8265 (mttp) cc_final: 0.8005 (pttp) REVERT: D 971 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: D 1035 ASP cc_start: 0.7244 (t0) cc_final: 0.6980 (t0) outliers start: 27 outliers final: 20 residues processed: 247 average time/residue: 0.6670 time to fit residues: 196.1269 Evaluate side-chains 250 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 971 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 220 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 380 optimal weight: 0.9990 chunk 297 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** 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 = 0.4366 r_free = 0.4366 target = 0.198212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119677 restraints weight = 65279.382| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.19 r_work: 0.3127 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32592 Z= 0.174 Angle : 0.630 17.480 44156 Z= 0.311 Chirality : 0.047 0.520 4912 Planarity : 0.004 0.040 5652 Dihedral : 6.728 68.239 4660 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.86 % Allowed : 13.45 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4068 helix: 0.65 (0.12), residues: 1776 sheet: -0.51 (0.24), residues: 536 loop : -1.07 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1085 TYR 0.027 0.002 TYR B 16 PHE 0.020 0.001 PHE D 354 TRP 0.006 0.001 TRP B 233 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd covalent geometry : bond 0.00425 (32592) covalent geometry : angle 0.62967 (44156) hydrogen bonds : bond 0.03490 ( 1418) hydrogen bonds : angle 4.38013 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13417.23 seconds wall clock time: 228 minutes 33.20 seconds (13713.20 seconds total)