Starting phenix.real_space_refine on Mon Jul 6 00:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lla_23413/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_2026/7lla_23413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lla_23413/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 12.92, per 1000 atoms: 0.41 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: 2.73 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: 1.34 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: 7.66 Time building geometry restraints manager: 3.64 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: 17888 20.78 - 41.56: 1269 41.56 - 62.35: 182 62.35 - 83.13: 37 83.13 - 103.91: 12 Dihedral angle restraints: 19388 sinusoidal: 7748 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 19385 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: 0.830 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.190 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 14.546 103.910 11996 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/Z covalent geometry : bond 0.00570 / 0.36 (32592) covalent geometry : angle 0.95828 / 0.56 (44156) hydrogen bonds : bond 0.15048 / 9.86 ( 1418) hydrogen bonds : angle 7.30747 / 5.12 ( 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 : 1.206 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: 0.6916 time to fit residues: 311.4321 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 : 1.257 ------------------------------------------------------------------------------- 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... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 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 = 0.4455 r_free = 0.4455 target = 0.211435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139265 restraints weight = 69626.182| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.78 r_work: 0.3382 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32592 Z= 0.120 Angle : 0.593 10.611 44156 Z= 0.304 Chirality : 0.045 0.154 4912 Planarity : 0.005 0.060 5652 Dihedral : 7.155 99.375 4519 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.16 % Allowed : 8.46 % Favored : 90.38 % 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: -1.29 (0.13), residues: 4068 helix: -0.32 (0.12), residues: 1768 sheet: -0.29 (0.23), residues: 560 loop : -1.53 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 561 TYR 0.016 0.001 TYR D 199 PHE 0.014 0.001 PHE D 191 TRP 0.013 0.001 TRP D 233 HIS 0.003 0.000 HIS D 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (32592) covalent geometry : angle 0.59259 / 0.30 (44156) hydrogen bonds : bond 0.03587 / 2.32 ( 1418) hydrogen bonds : angle 4.92596 / 3.48 ( 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 313 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.264 Fit side-chains REVERT: A 197 PHE cc_start: 0.7861 (m-10) cc_final: 0.7653 (m-10) REVERT: A 364 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5915 (t80) REVERT: A 491 THR cc_start: 0.8389 (m) cc_final: 0.8112 (t) REVERT: A 614 ASP cc_start: 0.7992 (m-30) cc_final: 0.7780 (m-30) REVERT: A 698 MET cc_start: 0.7250 (mmm) cc_final: 0.6998 (mmm) REVERT: B 614 ASP cc_start: 0.7814 (m-30) cc_final: 0.7453 (m-30) REVERT: C 195 LEU cc_start: 0.7360 (tm) cc_final: 0.7115 (tm) REVERT: C 197 PHE cc_start: 0.7966 (m-10) cc_final: 0.7527 (m-10) REVERT: C 1035 ASP cc_start: 0.7701 (t0) cc_final: 0.7481 (t0) REVERT: D 1035 ASP cc_start: 0.7511 (t0) cc_final: 0.7274 (t0) outliers start: 39 outliers final: 11 residues processed: 289 average time/residue: 0.6024 time to fit residues: 212.5056 Evaluate side-chains 270 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 258 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 B residue 728 CYS Chi-restraints excluded: chain B residue 1036 MET 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: 0.8980 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 0.0030 chunk 377 optimal weight: 1.9990 chunk 172 optimal weight: 0.2980 chunk 116 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 997 HIS C 975 HIS ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 996 GLN D 997 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.211341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136892 restraints weight = 69535.310| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.80 r_work: 0.3368 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32592 Z= 0.106 Angle : 0.549 10.216 44156 Z= 0.279 Chirality : 0.044 0.177 4912 Planarity : 0.004 0.051 5652 Dihedral : 6.628 90.196 4500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.04 % Allowed : 9.71 % Favored : 89.25 % 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: -0.77 (0.13), residues: 4068 helix: 0.24 (0.12), residues: 1784 sheet: -0.31 (0.24), residues: 560 loop : -1.31 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 703 TYR 0.025 0.001 TYR B 16 PHE 0.011 0.001 PHE D 863 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.000 HIS C 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (32592) covalent geometry : angle 0.54933 / 0.28 (44156) hydrogen bonds : bond 0.03248 / 2.12 ( 1418) hydrogen bonds : angle 4.50105 / 3.18 ( 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 304 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7622 (m-10) cc_final: 0.7353 (m-10) REVERT: A 364 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5852 (t80) REVERT: A 491 THR cc_start: 0.8458 (m) cc_final: 0.8220 (t) REVERT: A 614 ASP cc_start: 0.7968 (m-30) cc_final: 0.7725 (m-30) REVERT: A 712 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7947 (ptm) REVERT: A 1035 ASP cc_start: 0.7861 (t0) cc_final: 0.7634 (t0) REVERT: B 614 ASP cc_start: 0.7801 (m-30) cc_final: 0.7423 (m-30) REVERT: C 268 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5674 (mp) REVERT: C 698 MET cc_start: 0.6977 (mmm) cc_final: 0.6651 (mmm) REVERT: C 977 VAL cc_start: 0.8154 (m) cc_final: 0.7920 (p) REVERT: C 1035 ASP cc_start: 0.7773 (t0) cc_final: 0.7544 (t0) REVERT: D 197 PHE cc_start: 0.7867 (m-10) cc_final: 0.7453 (m-10) REVERT: D 545 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6720 (p-80) REVERT: D 733 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7398 (mt-10) REVERT: D 971 MET cc_start: 0.8375 (ttm) cc_final: 0.8080 (ttt) REVERT: D 1035 ASP cc_start: 0.7562 (t0) cc_final: 0.7334 (t0) outliers start: 35 outliers final: 11 residues processed: 284 average time/residue: 0.6221 time to fit residues: 215.2829 Evaluate side-chains 266 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 712 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 C residue 195 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 545 HIS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 68 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 315 optimal weight: 30.0000 chunk 317 optimal weight: 20.0000 chunk 341 optimal weight: 4.9990 chunk 365 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** 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 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 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 = 0.4421 r_free = 0.4421 target = 0.207896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130488 restraints weight = 64141.335| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.67 r_work: 0.3278 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2035 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= 0.157 Angle : 0.592 12.302 44156 Z= 0.298 Chirality : 0.046 0.335 4912 Planarity : 0.004 0.047 5652 Dihedral : 6.411 89.506 4498 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.45 % Allowed : 10.78 % Favored : 87.77 % 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: -0.63 (0.13), residues: 4068 helix: 0.39 (0.12), residues: 1776 sheet: -0.32 (0.24), residues: 560 loop : -1.24 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 703 TYR 0.015 0.002 TYR C 885 PHE 0.015 0.001 PHE B 376 TRP 0.006 0.001 TRP C 233 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (32592) covalent geometry : angle 0.59207 / 0.30 (44156) hydrogen bonds : bond 0.03453 / 2.26 ( 1418) hydrogen bonds : angle 4.48176 / 3.16 ( 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 311 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7364 (m-10) cc_final: 0.7159 (m-10) REVERT: A 364 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5857 (t80) REVERT: A 385 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7283 (mm-40) REVERT: A 491 THR cc_start: 0.8594 (m) cc_final: 0.8365 (t) REVERT: A 545 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6920 (p-80) REVERT: A 614 ASP cc_start: 0.8058 (m-30) cc_final: 0.7839 (m-30) REVERT: A 1035 ASP cc_start: 0.7911 (t0) cc_final: 0.7664 (t0) REVERT: B 614 ASP cc_start: 0.7928 (m-30) cc_final: 0.7556 (m-30) REVERT: B 777 GLN cc_start: 0.7628 (pp30) cc_final: 0.7371 (pt0) REVERT: C 545 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6807 (p-80) REVERT: C 971 MET cc_start: 0.8588 (ttm) cc_final: 0.8321 (ttt) REVERT: C 1035 ASP cc_start: 0.7764 (t0) cc_final: 0.7525 (t0) REVERT: D 197 PHE cc_start: 0.7975 (m-10) cc_final: 0.7739 (m-10) REVERT: D 391 MET cc_start: 0.6425 (mmm) cc_final: 0.6188 (mmm) REVERT: D 777 GLN cc_start: 0.7695 (pp30) cc_final: 0.7283 (pt0) REVERT: D 971 MET cc_start: 0.8549 (ttm) cc_final: 0.8303 (ttt) REVERT: D 1035 ASP cc_start: 0.7671 (t0) cc_final: 0.7433 (t0) outliers start: 49 outliers final: 23 residues processed: 288 average time/residue: 0.5788 time to fit residues: 202.9060 Evaluate side-chains 272 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 287 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 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 C residue 195 LEU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS 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 925 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 1036 MET 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: 0.9980 chunk 214 optimal weight: 8.9990 chunk 362 optimal weight: 4.9990 chunk 224 optimal weight: 0.4980 chunk 294 optimal weight: 4.9990 chunk 380 optimal weight: 8.9990 chunk 378 optimal weight: 5.9990 chunk 385 optimal weight: 0.6980 chunk 286 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 668 ASN ** A 879 GLN ** 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 975 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.201731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115502 restraints weight = 68196.739| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.28 r_work: 0.3258 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32592 Z= 0.131 Angle : 0.571 13.150 44156 Z= 0.286 Chirality : 0.045 0.350 4912 Planarity : 0.004 0.043 5652 Dihedral : 6.170 87.178 4498 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.25 % Allowed : 11.70 % Favored : 87.05 % 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: -0.50 (0.13), residues: 4068 helix: 0.55 (0.13), residues: 1780 sheet: -0.30 (0.24), residues: 560 loop : -1.22 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.001 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (32592) covalent geometry : angle 0.57124 / 0.29 (44156) hydrogen bonds : bond 0.03259 / 2.15 ( 1418) hydrogen bonds : angle 4.35573 / 3.07 ( 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 292 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5747 (t80) REVERT: A 491 THR cc_start: 0.8443 (m) cc_final: 0.8213 (t) REVERT: A 545 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6633 (p-80) REVERT: A 614 ASP cc_start: 0.7731 (m-30) cc_final: 0.7491 (m-30) REVERT: A 1035 ASP cc_start: 0.7352 (t0) cc_final: 0.7088 (t0) REVERT: B 545 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.6637 (p-80) REVERT: B 732 LYS cc_start: 0.7385 (mtmm) cc_final: 0.7148 (mmpt) REVERT: B 777 GLN cc_start: 0.7525 (pp30) cc_final: 0.7241 (pt0) REVERT: C 545 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6703 (p-80) REVERT: C 777 GLN cc_start: 0.7432 (pp30) cc_final: 0.7173 (pt0) REVERT: C 971 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8127 (ttt) REVERT: C 1035 ASP cc_start: 0.7132 (t0) cc_final: 0.6881 (t0) REVERT: D 971 MET cc_start: 0.8376 (ttm) cc_final: 0.8054 (ttt) REVERT: D 1035 ASP cc_start: 0.7116 (t0) cc_final: 0.6867 (t0) outliers start: 42 outliers final: 15 residues processed: 272 average time/residue: 0.6187 time to fit residues: 202.7577 Evaluate side-chains 252 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1036 MET 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 1036 MET Chi-restraints excluded: chain C residue 195 LEU 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 971 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 79 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 351 optimal weight: 3.9990 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: 5.9990 chunk 303 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 668 ASN A 777 GLN ** A 879 GLN ** 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 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 668 ASN ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.197891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111135 restraints weight = 60024.528| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.04 r_work: 0.3205 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32592 Z= 0.202 Angle : 0.627 13.470 44156 Z= 0.316 Chirality : 0.048 0.386 4912 Planarity : 0.004 0.042 5652 Dihedral : 6.181 86.079 4496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.31 % Allowed : 12.08 % 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: -0.60 (0.13), residues: 4068 helix: 0.45 (0.12), residues: 1780 sheet: -0.40 (0.24), residues: 560 loop : -1.22 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 703 TYR 0.017 0.002 TYR D 885 PHE 0.025 0.002 PHE A 197 TRP 0.006 0.001 TRP B 877 HIS 0.005 0.001 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 (32592) covalent geometry : angle 0.62669 / 0.32 (44156) hydrogen bonds : bond 0.03684 / 2.42 ( 1418) hydrogen bonds : angle 4.50914 / 3.18 ( 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 276 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.7270 (t) cc_final: 0.6913 (t) REVERT: A 364 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5755 (t80) REVERT: A 491 THR cc_start: 0.8519 (m) cc_final: 0.8318 (t) REVERT: B 545 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6967 (p-80) REVERT: B 732 LYS cc_start: 0.7368 (mtmm) cc_final: 0.7142 (mmpt) REVERT: B 777 GLN cc_start: 0.7566 (pp30) cc_final: 0.7291 (pt0) REVERT: B 971 MET cc_start: 0.8438 (ttm) cc_final: 0.8066 (ttt) REVERT: C 545 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6954 (p-80) REVERT: C 971 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8260 (ttt) REVERT: C 1035 ASP cc_start: 0.7335 (t0) cc_final: 0.7072 (t0) REVERT: D 732 LYS cc_start: 0.7264 (mtmm) cc_final: 0.7011 (mmpt) REVERT: D 777 GLN cc_start: 0.7272 (pp30) cc_final: 0.6965 (pt0) REVERT: D 971 MET cc_start: 0.8567 (ttm) cc_final: 0.8233 (ttt) REVERT: D 1035 ASP cc_start: 0.7364 (t0) cc_final: 0.7092 (t0) outliers start: 44 outliers final: 22 residues processed: 257 average time/residue: 0.6193 time to fit residues: 190.6688 Evaluate side-chains 248 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG 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 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 1024 ASN 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 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 702 LEU 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 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: 0.6980 chunk 79 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 351 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 777 GLN A 879 GLN ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN C 777 GLN C 879 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 668 ASN ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 879 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.204249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115405 restraints weight = 57780.575| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.14 r_work: 0.3291 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32592 Z= 0.105 Angle : 0.566 14.890 44156 Z= 0.283 Chirality : 0.044 0.346 4912 Planarity : 0.004 0.040 5652 Dihedral : 5.861 83.807 4496 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.04 % Allowed : 12.53 % Favored : 86.43 % 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: -0.35 (0.13), residues: 4068 helix: 0.70 (0.13), residues: 1780 sheet: -0.28 (0.24), residues: 560 loop : -1.15 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 703 TYR 0.026 0.001 TYR B 16 PHE 0.017 0.001 PHE B 354 TRP 0.007 0.001 TRP A 276 HIS 0.002 0.000 HIS C 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (32592) covalent geometry : angle 0.56649 / 0.28 (44156) hydrogen bonds : bond 0.03071 / 2.03 ( 1418) hydrogen bonds : angle 4.29485 / 3.04 ( 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 273 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5599 (mtp85) REVERT: A 364 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5762 (t80) REVERT: B 545 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6811 (p-80) REVERT: B 777 GLN cc_start: 0.7557 (pp30) cc_final: 0.7301 (pt0) REVERT: B 881 ARG cc_start: 0.8246 (ttp80) cc_final: 0.8043 (mtp180) REVERT: B 971 MET cc_start: 0.8337 (ttm) cc_final: 0.7937 (ttt) REVERT: B 1024 ASN cc_start: 0.7952 (m110) cc_final: 0.7586 (p0) REVERT: C 545 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6768 (p-80) REVERT: C 732 LYS cc_start: 0.7458 (mtmm) cc_final: 0.7222 (mmpt) REVERT: C 971 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8091 (ttt) REVERT: C 1035 ASP cc_start: 0.6994 (t0) cc_final: 0.6736 (t0) REVERT: D 391 MET cc_start: 0.5676 (mmm) cc_final: 0.5423 (mmm) REVERT: D 732 LYS cc_start: 0.7234 (mtmm) cc_final: 0.6940 (mmpt) REVERT: D 777 GLN cc_start: 0.7359 (pp30) cc_final: 0.7014 (pt0) REVERT: D 971 MET cc_start: 0.8456 (ttm) cc_final: 0.8093 (ttt) REVERT: D 1035 ASP cc_start: 0.7024 (t0) cc_final: 0.6768 (t0) outliers start: 35 outliers final: 16 residues processed: 260 average time/residue: 0.6720 time to fit residues: 208.9859 Evaluate side-chains 243 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 364 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 371 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 668 ASN A 777 GLN ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 668 ASN ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.202090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124406 restraints weight = 80571.170| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.38 r_work: 0.3159 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32592 Z= 0.152 Angle : 0.604 17.166 44156 Z= 0.299 Chirality : 0.046 0.373 4912 Planarity : 0.004 0.039 5652 Dihedral : 5.856 83.583 4496 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.95 % Allowed : 13.18 % Favored : 85.87 % 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: -0.33 (0.13), residues: 4068 helix: 0.68 (0.12), residues: 1780 sheet: -0.26 (0.24), residues: 560 loop : -1.09 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1085 TYR 0.013 0.001 TYR D 124 PHE 0.018 0.001 PHE B 354 TRP 0.007 0.001 TRP B 233 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (32592) covalent geometry : angle 0.60421 / 0.30 (44156) hydrogen bonds : bond 0.03313 / 2.18 ( 1418) hydrogen bonds : angle 4.32490 / 3.05 ( 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 259 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5557 (mtp85) REVERT: B 196 TYR cc_start: 0.6455 (m-80) cc_final: 0.6090 (m-80) REVERT: B 777 GLN cc_start: 0.7586 (pp30) cc_final: 0.7324 (pt0) REVERT: B 881 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8167 (mtp180) REVERT: B 971 MET cc_start: 0.8500 (ttm) cc_final: 0.8122 (ttt) REVERT: C 197 PHE cc_start: 0.7791 (m-10) cc_final: 0.7546 (m-10) REVERT: C 545 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6951 (p-80) REVERT: C 732 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7275 (mmpt) REVERT: C 777 GLN cc_start: 0.7811 (pp30) cc_final: 0.7394 (pt0) REVERT: C 971 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8263 (ttt) REVERT: C 978 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6618 (mtpm) REVERT: C 1035 ASP cc_start: 0.7317 (t0) cc_final: 0.7034 (t0) REVERT: D 391 MET cc_start: 0.5696 (mmm) cc_final: 0.5429 (mmm) REVERT: D 732 LYS cc_start: 0.7316 (mtmm) cc_final: 0.7054 (mmpt) REVERT: D 777 GLN cc_start: 0.7394 (pp30) cc_final: 0.7032 (pt0) REVERT: D 965 LYS cc_start: 0.8314 (mttp) cc_final: 0.8030 (pttp) REVERT: D 971 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8230 (ttt) REVERT: D 1035 ASP cc_start: 0.7296 (t0) cc_final: 0.7023 (t0) outliers start: 32 outliers final: 19 residues processed: 244 average time/residue: 0.6389 time to fit residues: 186.7811 Evaluate side-chains 246 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR 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 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 971 MET Chi-restraints excluded: chain C residue 978 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 313 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 209 optimal weight: 30.0000 chunk 336 optimal weight: 30.0000 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 668 ASN A 777 GLN ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.200817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122050 restraints weight = 65805.853| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.77 r_work: 0.3132 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2787 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= 0.174 Angle : 0.630 16.285 44156 Z= 0.312 Chirality : 0.047 0.434 4912 Planarity : 0.004 0.040 5652 Dihedral : 5.922 82.740 4496 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.89 % Allowed : 13.45 % Favored : 85.66 % 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: -0.39 (0.13), residues: 4068 helix: 0.60 (0.12), residues: 1780 sheet: -0.28 (0.24), residues: 560 loop : -1.11 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1085 TYR 0.026 0.002 TYR B 16 PHE 0.019 0.001 PHE D 354 TRP 0.005 0.001 TRP B 233 HIS 0.004 0.001 HIS C 975 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (32592) covalent geometry : angle 0.63040 / 0.31 (44156) hydrogen bonds : bond 0.03506 / 2.31 ( 1418) hydrogen bonds : angle 4.41977 / 3.12 ( 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 255 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5534 (mtp85) REVERT: A 732 LYS cc_start: 0.7523 (mtmm) cc_final: 0.7262 (mmpt) REVERT: B 777 GLN cc_start: 0.7609 (pp30) cc_final: 0.7315 (pt0) REVERT: B 881 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8147 (mtp180) REVERT: B 971 MET cc_start: 0.8525 (ttm) cc_final: 0.8174 (ttt) REVERT: C 197 PHE cc_start: 0.7823 (m-10) cc_final: 0.7437 (m-10) REVERT: C 732 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7250 (mmtm) REVERT: C 777 GLN cc_start: 0.7823 (pp30) cc_final: 0.7422 (pt0) REVERT: C 971 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8297 (ttt) REVERT: C 1035 ASP cc_start: 0.7360 (t0) cc_final: 0.7089 (t0) REVERT: D 391 MET cc_start: 0.5664 (mmm) cc_final: 0.5362 (mmm) REVERT: D 777 GLN cc_start: 0.7422 (pp30) cc_final: 0.7056 (pt0) REVERT: D 971 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8247 (ttt) REVERT: D 1035 ASP cc_start: 0.7329 (t0) cc_final: 0.7064 (t0) outliers start: 30 outliers final: 20 residues processed: 243 average time/residue: 0.6997 time to fit residues: 203.0228 Evaluate side-chains 241 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR 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 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 Chi-restraints excluded: chain D residue 1036 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: 30.0000 chunk 266 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 300 optimal weight: 4.9990 chunk 359 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 345 optimal weight: 30.0000 chunk 350 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN A 668 ASN ** 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 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116697 restraints weight = 75497.880| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 5.17 r_work: 0.3103 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32592 Z= 0.200 Angle : 0.647 17.052 44156 Z= 0.320 Chirality : 0.048 0.483 4912 Planarity : 0.004 0.040 5652 Dihedral : 5.967 82.738 4496 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.77 % Allowed : 13.78 % Favored : 85.45 % 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: -0.46 (0.13), residues: 4068 helix: 0.54 (0.12), residues: 1776 sheet: -0.34 (0.24), residues: 560 loop : -1.12 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1085 TYR 0.018 0.002 TYR A 307 PHE 0.021 0.002 PHE A 354 TRP 0.008 0.001 TRP B 276 HIS 0.004 0.001 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (32592) covalent geometry : angle 0.64651 / 0.32 (44156) hydrogen bonds : bond 0.03664 / 2.42 ( 1418) hydrogen bonds : angle 4.48168 / 3.16 ( 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 255 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 732 LYS cc_start: 0.7408 (mtmm) cc_final: 0.7185 (mmpt) REVERT: B 881 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8101 (mtp180) REVERT: B 971 MET cc_start: 0.8459 (ttm) cc_final: 0.8120 (ttt) REVERT: C 197 PHE cc_start: 0.7692 (m-10) cc_final: 0.7419 (m-10) REVERT: C 732 LYS cc_start: 0.7450 (mtmm) cc_final: 0.7163 (mmtm) REVERT: C 777 GLN cc_start: 0.7793 (pp30) cc_final: 0.7389 (pt0) REVERT: C 971 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8228 (ttt) REVERT: C 1035 ASP cc_start: 0.7281 (t0) cc_final: 0.7013 (t0) REVERT: D 391 MET cc_start: 0.5593 (mmm) cc_final: 0.5317 (mmm) REVERT: D 732 LYS cc_start: 0.7261 (mtmm) cc_final: 0.6962 (mmpt) REVERT: D 965 LYS cc_start: 0.8185 (mttp) cc_final: 0.7902 (pttp) REVERT: D 971 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8214 (ttt) REVERT: D 1035 ASP cc_start: 0.7297 (t0) cc_final: 0.7027 (t0) outliers start: 26 outliers final: 20 residues processed: 247 average time/residue: 0.7503 time to fit residues: 218.9087 Evaluate side-chains 242 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR 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 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 Chi-restraints excluded: chain D residue 1036 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: 7.9990 chunk 377 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 327 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 chunk 376 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 380 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 668 ASN ** 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 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 668 ASN D 777 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.198431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111712 restraints weight = 65266.851| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.23 r_work: 0.3201 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32592 Z= 0.164 Angle : 0.634 17.938 44156 Z= 0.313 Chirality : 0.047 0.470 4912 Planarity : 0.004 0.041 5652 Dihedral : 5.907 82.382 4496 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.77 % Allowed : 13.98 % Favored : 85.24 % 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: -0.34 (0.24), residues: 560 loop : -1.11 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1045 TYR 0.021 0.002 TYR B 16 PHE 0.023 0.001 PHE A 354 TRP 0.006 0.001 TRP B 233 HIS 0.003 0.001 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (32592) covalent geometry : angle 0.63407 / 0.31 (44156) hydrogen bonds : bond 0.03475 / 2.30 ( 1418) hydrogen bonds : angle 4.43561 / 3.13 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12555.30 seconds wall clock time: 214 minutes 30.44 seconds (12870.44 seconds total)