Starting phenix.real_space_refine on Thu Mar 5 04:14:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnh_33315/03_2026/7xnh_33315.map" } resolution = 3.1 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 13212 2.51 5 N 2820 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19224 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "C" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "L" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 158 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-1': 12, 'MC3:plan-2': 12} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'MC3': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 10, 'MC3:plan-2': 10} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 158 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-1': 12, 'MC3:plan-2': 12} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'MC3': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 10, 'MC3:plan-2': 10} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 4.08, per 1000 atoms: 0.21 Number of scatterers: 19224 At special positions: 0 Unit cell: (94.752, 100.674, 145.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3036 8.00 N 2820 7.00 C 13212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 778.0 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 74.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.235A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 221 Processing helix chain 'A' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.183A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.234A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.653A pdb=" N PHE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 221 Processing helix chain 'C' and resid 246 through 276 removed outlier: 3.651A pdb=" N PHE C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.234A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 221 Processing helix chain 'D' and resid 246 through 276 removed outlier: 3.651A pdb=" N PHE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 4.183A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 41 through 46 removed outlier: 4.234A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 87 through 101 removed outlier: 4.105A pdb=" N PHE E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 221 Processing helix chain 'E' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 34 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.234A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER F 101 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 221 Processing helix chain 'F' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.651A pdb=" N PHE G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 removed outlier: 4.185A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 13 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 34 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 87 through 101 removed outlier: 4.105A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 100 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 221 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA I 13 " --> pdb=" O ARG I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.234A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 87 through 101 removed outlier: 4.105A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN I 100 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 4.183A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA J 13 " --> pdb=" O ARG J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN J 100 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER J 101 " --> pdb=" O SER J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.652A pdb=" N PHE J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 13 removed outlier: 4.184A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA K 13 " --> pdb=" O ARG K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 87 Processing helix chain 'K' and resid 87 through 101 removed outlier: 4.105A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.651A pdb=" N PHE K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 removed outlier: 4.183A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA L 13 " --> pdb=" O ARG L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 46 removed outlier: 4.233A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 87 Processing helix chain 'L' and resid 87 through 101 removed outlier: 4.104A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL L 98 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN L 100 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.651A pdb=" N PHE L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 1104 hydrogen bonds defined for protein. 3240 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: 3.05 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5389 1.34 - 1.46: 4167 1.46 - 1.58: 9752 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 19512 Sorted by residual: bond pdb=" CB PRO B 235 " pdb=" CG PRO B 235 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.61e+00 bond pdb=" CB PRO L 235 " pdb=" CG PRO L 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CB PRO H 235 " pdb=" CG PRO H 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CB PRO C 235 " pdb=" CG PRO C 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" CB PRO J 235 " pdb=" CG PRO J 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 19507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 22353 1.14 - 2.28: 1767 2.28 - 3.42: 593 3.42 - 4.56: 854 4.56 - 5.70: 269 Bond angle restraints: 25836 Sorted by residual: angle pdb=" N PHE G 253 " pdb=" CA PHE G 253 " pdb=" CB PHE G 253 " ideal model delta sigma weight residual 110.12 114.24 -4.12 1.47e+00 4.63e-01 7.84e+00 angle pdb=" N PHE H 253 " pdb=" CA PHE H 253 " pdb=" CB PHE H 253 " ideal model delta sigma weight residual 110.12 114.24 -4.12 1.47e+00 4.63e-01 7.84e+00 angle pdb=" N PHE A 253 " pdb=" CA PHE A 253 " pdb=" CB PHE A 253 " ideal model delta sigma weight residual 110.12 114.23 -4.11 1.47e+00 4.63e-01 7.81e+00 angle pdb=" N PHE D 253 " pdb=" CA PHE D 253 " pdb=" CB PHE D 253 " ideal model delta sigma weight residual 110.12 114.22 -4.10 1.47e+00 4.63e-01 7.80e+00 angle pdb=" N PHE J 253 " pdb=" CA PHE J 253 " pdb=" CB PHE J 253 " ideal model delta sigma weight residual 110.12 114.22 -4.10 1.47e+00 4.63e-01 7.79e+00 ... (remaining 25831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 10692 14.58 - 29.17: 720 29.17 - 43.75: 228 43.75 - 58.34: 180 58.34 - 72.92: 36 Dihedral angle restraints: 11856 sinusoidal: 5484 harmonic: 6372 Sorted by residual: dihedral pdb=" CB GLU I 239 " pdb=" CG GLU I 239 " pdb=" CD GLU I 239 " pdb=" OE1 GLU I 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.92 72.92 1 3.00e+01 1.11e-03 7.53e+00 dihedral pdb=" CB GLU F 239 " pdb=" CG GLU F 239 " pdb=" CD GLU F 239 " pdb=" OE1 GLU F 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.89 72.89 1 3.00e+01 1.11e-03 7.53e+00 dihedral pdb=" CB GLU L 239 " pdb=" CG GLU L 239 " pdb=" CD GLU L 239 " pdb=" OE1 GLU L 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.89 72.89 1 3.00e+01 1.11e-03 7.53e+00 ... (remaining 11853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1765 0.038 - 0.076: 773 0.076 - 0.114: 212 0.114 - 0.153: 82 0.153 - 0.191: 12 Chirality restraints: 2844 Sorted by residual: chirality pdb=" CA PHE A 253 " pdb=" N PHE A 253 " pdb=" C PHE A 253 " pdb=" CB PHE A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA PHE G 253 " pdb=" N PHE G 253 " pdb=" C PHE G 253 " pdb=" CB PHE G 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PHE B 253 " pdb=" N PHE B 253 " pdb=" C PHE B 253 " pdb=" CB PHE B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 2841 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 23 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C GLY L 23 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY L 23 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG L 24 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 23 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLY H 23 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY H 23 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG H 24 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 23 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLY B 23 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY B 23 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 24 " 0.013 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 379 2.70 - 3.25: 16925 3.25 - 3.80: 28824 3.80 - 4.35: 39435 4.35 - 4.90: 68176 Nonbonded interactions: 153739 Sorted by model distance: nonbonded pdb=" OE1 GLU E 230 " pdb=" NZ LYS L 238 " model vdw 2.144 3.120 nonbonded pdb=" OE1 GLU F 230 " pdb=" NZ LYS K 238 " model vdw 2.157 3.120 nonbonded pdb=" NZ LYS E 238 " pdb=" OE1 GLU L 230 " model vdw 2.190 3.120 nonbonded pdb=" NZ LYS D 238 " pdb=" OE1 GLU G 230 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS F 238 " pdb=" OE1 GLU K 230 " model vdw 2.239 3.120 ... (remaining 153734 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 0.050 19560 Z= 0.247 Angle : 1.121 5.704 25908 Z= 0.495 Chirality : 0.048 0.191 2844 Planarity : 0.006 0.053 3024 Dihedral : 13.571 72.920 7644 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.61 % Allowed : 0.61 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.23 (0.16), residues: 2124 helix: 0.23 (0.13), residues: 1392 sheet: 1.30 (0.47), residues: 144 loop : -1.23 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 77 TYR 0.016 0.003 TYR A 67 PHE 0.017 0.002 PHE F 253 TRP 0.006 0.001 TRP I 79 HIS 0.002 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00561 (19512) covalent geometry : angle 1.11932 (25836) SS BOND : bond 0.00534 ( 36) SS BOND : angle 1.61969 ( 72) hydrogen bonds : bond 0.15133 ( 1104) hydrogen bonds : angle 5.08966 ( 3240) Misc. bond : bond 0.00058 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 416 time to evaluate : 0.677 Fit side-chains REVERT: C 27 LEU cc_start: 0.7889 (mp) cc_final: 0.7455 (mt) REVERT: I 257 MET cc_start: 0.8901 (mmt) cc_final: 0.8320 (mmt) outliers start: 12 outliers final: 9 residues processed: 419 average time/residue: 0.1378 time to fit residues: 87.4078 Evaluate side-chains 371 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 362 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 238 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 50 GLN C 50 GLN C 99 HIS D 50 GLN D 99 HIS E 50 GLN E 99 HIS F 50 GLN F 99 HIS G 50 GLN G 63 ASN H 50 GLN I 50 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN J 63 ASN K 50 GLN L 50 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.111985 restraints weight = 17123.894| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.80 r_work: 0.2567 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19560 Z= 0.152 Angle : 0.520 4.820 25908 Z= 0.277 Chirality : 0.042 0.142 2844 Planarity : 0.005 0.035 3024 Dihedral : 14.468 59.996 3744 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.77 % Allowed : 3.94 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.39 (0.17), residues: 2124 helix: 1.57 (0.14), residues: 1392 sheet: 1.61 (0.45), residues: 144 loop : -0.79 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 24 TYR 0.014 0.002 TYR G 67 PHE 0.008 0.001 PHE G 198 TRP 0.006 0.001 TRP D 79 HIS 0.003 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (19512) covalent geometry : angle 0.51710 (25836) SS BOND : bond 0.00383 ( 36) SS BOND : angle 1.17278 ( 72) hydrogen bonds : bond 0.05969 ( 1104) hydrogen bonds : angle 3.69316 ( 3240) Misc. bond : bond 0.00032 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 361 time to evaluate : 0.678 Fit side-chains REVERT: A 3 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 34 ARG cc_start: 0.8867 (mtt180) cc_final: 0.8601 (mtt180) REVERT: K 34 ARG cc_start: 0.8861 (mtt180) cc_final: 0.8639 (mtt180) REVERT: L 257 MET cc_start: 0.9167 (mmt) cc_final: 0.8743 (mmt) outliers start: 15 outliers final: 10 residues processed: 367 average time/residue: 0.1276 time to fit residues: 72.7864 Evaluate side-chains 344 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 334 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 125 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.152437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.143512 restraints weight = 16936.162| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.44 r_work: 0.3289 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19560 Z= 0.165 Angle : 0.524 4.697 25908 Z= 0.276 Chirality : 0.043 0.151 2844 Planarity : 0.004 0.033 3024 Dihedral : 13.480 59.922 3708 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.38 % Allowed : 5.37 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.91 (0.17), residues: 2124 helix: 1.95 (0.14), residues: 1392 sheet: 1.38 (0.44), residues: 144 loop : -0.40 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 77 TYR 0.014 0.002 TYR G 67 PHE 0.007 0.001 PHE D 71 TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00398 (19512) covalent geometry : angle 0.52042 (25836) SS BOND : bond 0.00440 ( 36) SS BOND : angle 1.23704 ( 72) hydrogen bonds : bond 0.05974 ( 1104) hydrogen bonds : angle 3.56363 ( 3240) Misc. bond : bond 0.00017 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 347 time to evaluate : 0.509 Fit side-chains REVERT: D 34 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8671 (mtt180) REVERT: F 257 MET cc_start: 0.9129 (mmt) cc_final: 0.8706 (mmt) REVERT: L 257 MET cc_start: 0.9134 (mmt) cc_final: 0.8844 (mmt) outliers start: 27 outliers final: 14 residues processed: 359 average time/residue: 0.1307 time to fit residues: 72.4508 Evaluate side-chains 349 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 31 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 188 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.152647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.116325 restraints weight = 17077.718| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.55 r_work: 0.2621 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19560 Z= 0.112 Angle : 0.446 4.638 25908 Z= 0.237 Chirality : 0.040 0.142 2844 Planarity : 0.003 0.021 3024 Dihedral : 12.874 59.945 3708 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.48 % Allowed : 6.90 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.17), residues: 2124 helix: 2.34 (0.14), residues: 1392 sheet: 1.39 (0.43), residues: 144 loop : -0.26 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.011 0.001 TYR D 67 PHE 0.005 0.001 PHE H 198 TRP 0.003 0.001 TRP H 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00254 (19512) covalent geometry : angle 0.44389 (25836) SS BOND : bond 0.00249 ( 36) SS BOND : angle 0.98176 ( 72) hydrogen bonds : bond 0.04972 ( 1104) hydrogen bonds : angle 3.44287 ( 3240) Misc. bond : bond 0.00006 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 351 time to evaluate : 0.677 Fit side-chains REVERT: B 34 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8530 (mtt180) REVERT: D 34 ARG cc_start: 0.8838 (mtt180) cc_final: 0.8618 (mtt180) REVERT: D 82 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: F 257 MET cc_start: 0.9152 (mmt) cc_final: 0.8769 (mmt) REVERT: I 204 VAL cc_start: 0.8517 (t) cc_final: 0.8299 (m) outliers start: 29 outliers final: 17 residues processed: 364 average time/residue: 0.1264 time to fit residues: 71.5256 Evaluate side-chains 358 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 340 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.152892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.145455 restraints weight = 16930.349| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 0.23 r_work: 0.3370 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19560 Z= 0.113 Angle : 0.443 4.609 25908 Z= 0.235 Chirality : 0.041 0.144 2844 Planarity : 0.003 0.021 3024 Dihedral : 12.371 59.992 3708 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.43 % Allowed : 8.38 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.79 (0.17), residues: 2124 helix: 2.55 (0.13), residues: 1452 sheet: 1.42 (0.43), residues: 144 loop : -0.06 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.012 0.001 TYR A 67 PHE 0.005 0.001 PHE L 71 TRP 0.004 0.001 TRP L 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00260 (19512) covalent geometry : angle 0.44059 (25836) SS BOND : bond 0.00247 ( 36) SS BOND : angle 0.94004 ( 72) hydrogen bonds : bond 0.04773 ( 1104) hydrogen bonds : angle 3.37979 ( 3240) Misc. bond : bond 0.00008 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 351 time to evaluate : 0.463 Fit side-chains REVERT: D 34 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8586 (mtt180) outliers start: 28 outliers final: 17 residues processed: 363 average time/residue: 0.1267 time to fit residues: 71.5845 Evaluate side-chains 357 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 340 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.153337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.146563 restraints weight = 16857.975| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.44 r_work: 0.3353 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19560 Z= 0.106 Angle : 0.431 4.624 25908 Z= 0.230 Chirality : 0.040 0.140 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.953 59.859 3708 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.18 % Allowed : 9.25 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.94 (0.17), residues: 2124 helix: 2.68 (0.13), residues: 1452 sheet: 1.45 (0.43), residues: 144 loop : -0.04 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.011 0.001 TYR G 67 PHE 0.004 0.001 PHE A 53 TRP 0.003 0.001 TRP F 79 HIS 0.002 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00242 (19512) covalent geometry : angle 0.42905 (25836) SS BOND : bond 0.00221 ( 36) SS BOND : angle 0.91421 ( 72) hydrogen bonds : bond 0.04574 ( 1104) hydrogen bonds : angle 3.33592 ( 3240) Misc. bond : bond 0.00007 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 350 time to evaluate : 0.642 Fit side-chains REVERT: D 34 ARG cc_start: 0.8834 (mtt180) cc_final: 0.8607 (mtt180) outliers start: 23 outliers final: 16 residues processed: 358 average time/residue: 0.1258 time to fit residues: 70.0938 Evaluate side-chains 362 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 346 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 131 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.154271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.147393 restraints weight = 16920.148| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.46 r_work: 0.3355 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19560 Z= 0.099 Angle : 0.417 4.608 25908 Z= 0.224 Chirality : 0.040 0.138 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.539 59.704 3708 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.18 % Allowed : 9.87 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.04 (0.17), residues: 2124 helix: 2.73 (0.13), residues: 1464 sheet: 1.52 (0.44), residues: 144 loop : -0.02 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.010 0.001 TYR G 67 PHE 0.004 0.001 PHE F 53 TRP 0.003 0.001 TRP H 79 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00220 (19512) covalent geometry : angle 0.41559 (25836) SS BOND : bond 0.00189 ( 36) SS BOND : angle 0.83400 ( 72) hydrogen bonds : bond 0.04341 ( 1104) hydrogen bonds : angle 3.28466 ( 3240) Misc. bond : bond 0.00005 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 359 time to evaluate : 0.589 Fit side-chains REVERT: D 34 ARG cc_start: 0.8803 (mtt180) cc_final: 0.8536 (mtt180) outliers start: 23 outliers final: 17 residues processed: 366 average time/residue: 0.1191 time to fit residues: 68.5098 Evaluate side-chains 366 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 349 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 134 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.154786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.112929 restraints weight = 172406.096| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 7.40 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19560 Z= 0.092 Angle : 0.406 4.597 25908 Z= 0.218 Chirality : 0.039 0.134 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.145 59.816 3708 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.02 % Allowed : 10.38 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.12 (0.18), residues: 2124 helix: 2.81 (0.13), residues: 1464 sheet: 1.58 (0.44), residues: 144 loop : -0.05 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 24 TYR 0.009 0.001 TYR G 67 PHE 0.004 0.001 PHE A 53 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00198 (19512) covalent geometry : angle 0.40443 (25836) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.78858 ( 72) hydrogen bonds : bond 0.04088 ( 1104) hydrogen bonds : angle 3.24263 ( 3240) Misc. bond : bond 0.00003 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 356 time to evaluate : 0.670 Fit side-chains REVERT: D 34 ARG cc_start: 0.8595 (mtt180) cc_final: 0.8253 (mtt180) outliers start: 20 outliers final: 17 residues processed: 361 average time/residue: 0.1245 time to fit residues: 69.9319 Evaluate side-chains 368 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 351 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.143771 restraints weight = 16998.717| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 0.42 r_work: 0.3322 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19560 Z= 0.165 Angle : 0.508 4.697 25908 Z= 0.267 Chirality : 0.043 0.159 2844 Planarity : 0.004 0.030 3024 Dihedral : 11.771 59.071 3708 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.92 % Allowed : 10.02 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.63 (0.18), residues: 2124 helix: 2.59 (0.13), residues: 1452 sheet: -0.17 (0.38), residues: 204 loop : -0.12 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.016 0.002 TYR B 67 PHE 0.008 0.001 PHE C 71 TRP 0.005 0.001 TRP L 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00406 (19512) covalent geometry : angle 0.50491 (25836) SS BOND : bond 0.00405 ( 36) SS BOND : angle 1.15237 ( 72) hydrogen bonds : bond 0.05468 ( 1104) hydrogen bonds : angle 3.42457 ( 3240) Misc. bond : bond 0.00019 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 0.635 Fit side-chains REVERT: D 34 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8563 (mtt180) outliers start: 18 outliers final: 16 residues processed: 355 average time/residue: 0.1226 time to fit residues: 67.8016 Evaluate side-chains 366 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 350 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.151916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.145152 restraints weight = 16917.858| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.43 r_work: 0.3336 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19560 Z= 0.133 Angle : 0.467 4.648 25908 Z= 0.248 Chirality : 0.042 0.148 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.611 59.109 3708 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.92 % Allowed : 10.74 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.65 (0.18), residues: 2124 helix: 2.62 (0.13), residues: 1452 sheet: -0.11 (0.39), residues: 204 loop : -0.13 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 206 TYR 0.013 0.002 TYR A 67 PHE 0.005 0.001 PHE C 71 TRP 0.004 0.001 TRP H 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00317 (19512) covalent geometry : angle 0.46421 (25836) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.01682 ( 72) hydrogen bonds : bond 0.05052 ( 1104) hydrogen bonds : angle 3.37974 ( 3240) Misc. bond : bond 0.00013 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 357 time to evaluate : 0.735 Fit side-chains REVERT: D 34 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8560 (mtt180) outliers start: 18 outliers final: 16 residues processed: 360 average time/residue: 0.1189 time to fit residues: 66.8919 Evaluate side-chains 369 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 353 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 0.0000 chunk 191 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.154329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.111817 restraints weight = 171700.132| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 7.17 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19560 Z= 0.096 Angle : 0.412 4.618 25908 Z= 0.222 Chirality : 0.039 0.136 2844 Planarity : 0.003 0.021 3024 Dihedral : 10.882 59.195 3708 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.82 % Allowed : 10.94 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.11 (0.18), residues: 2124 helix: 2.80 (0.13), residues: 1464 sheet: 1.67 (0.46), residues: 144 loop : -0.05 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 233 TYR 0.008 0.001 TYR F 67 PHE 0.005 0.001 PHE L 198 TRP 0.003 0.001 TRP H 79 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00212 (19512) covalent geometry : angle 0.41000 (25836) SS BOND : bond 0.00178 ( 36) SS BOND : angle 0.80222 ( 72) hydrogen bonds : bond 0.04135 ( 1104) hydrogen bonds : angle 3.25977 ( 3240) Misc. bond : bond 0.00005 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.85 seconds wall clock time: 60 minutes 57.69 seconds (3657.69 seconds total)