Starting phenix.real_space_refine on Mon Jun 16 20:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_33315.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_33315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_33315.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_33315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnh_33315/06_2025/7xnh_33315.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 12, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 10, 'MC3:plan-1': 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-2': 12, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 12.47, per 1000 atoms: 0.65 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: 4.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.91 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: 5.57 Time building geometry restraints manager: 5.92 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } 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: 2.860 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: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 44.410 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.110 ------------------------------------------------------------------------------- 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 : 6.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.006 0.001 TRP I 79 HIS 0.002 0.001 HIS G 75 PHE 0.017 0.002 PHE F 253 TYR 0.016 0.003 TYR A 67 ARG 0.006 0.001 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.15133 ( 1104) hydrogen bonds : angle 5.08966 ( 3240) SS BOND : bond 0.00534 ( 36) SS BOND : angle 1.61969 ( 72) covalent geometry : bond 0.00561 (19512) covalent geometry : angle 1.11932 (25836) 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 : 2.214 Fit side-chains REVERT: C 27 LEU cc_start: 0.7889 (mp) cc_final: 0.7456 (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: 0.3263 time to fit residues: 205.2695 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 : 1.954 ------------------------------------------------------------------------------- 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 182 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 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 = 0.3543 r_free = 0.3543 target = 0.152641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.150065 restraints weight = 17149.975| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 0.12 r_work: 0.3466 rms_B_bonded: 0.35 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 0.76 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19560 Z= 0.130 Angle : 0.493 4.830 25908 Z= 0.262 Chirality : 0.041 0.141 2844 Planarity : 0.004 0.029 3024 Dihedral : 14.364 59.797 3744 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.72 % Allowed : 3.58 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2124 helix: 1.64 (0.14), residues: 1392 sheet: 1.54 (0.44), residues: 144 loop : -0.83 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 79 HIS 0.003 0.001 HIS D 75 PHE 0.008 0.001 PHE G 198 TYR 0.013 0.002 TYR G 67 ARG 0.003 0.000 ARG J 24 Details of bonding type rmsd hydrogen bonds : bond 0.05614 ( 1104) hydrogen bonds : angle 3.66976 ( 3240) SS BOND : bond 0.00297 ( 36) SS BOND : angle 1.03891 ( 72) covalent geometry : bond 0.00287 (19512) covalent geometry : angle 0.49048 (25836) Misc. bond : bond 0.00039 ( 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 383 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 369 time to evaluate : 2.194 Fit side-chains REVERT: I 257 MET cc_start: 0.9064 (mmt) cc_final: 0.8682 (mmt) REVERT: L 257 MET cc_start: 0.9107 (mmt) cc_final: 0.8643 (mmt) outliers start: 14 outliers final: 9 residues processed: 375 average time/residue: 0.3049 time to fit residues: 176.7842 Evaluate side-chains 348 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 339 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 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 85 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3519 r_free = 0.3519 target = 0.149651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.142701 restraints weight = 16903.205| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.45 r_work: 0.3305 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19560 Z= 0.204 Angle : 0.564 4.783 25908 Z= 0.295 Chirality : 0.045 0.157 2844 Planarity : 0.005 0.038 3024 Dihedral : 13.837 59.937 3708 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.33 % Allowed : 5.88 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2124 helix: 1.83 (0.14), residues: 1392 sheet: 1.36 (0.43), residues: 144 loop : -0.49 (0.19), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 79 HIS 0.003 0.001 HIS D 75 PHE 0.008 0.001 PHE L 71 TYR 0.017 0.002 TYR H 67 ARG 0.003 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.06487 ( 1104) hydrogen bonds : angle 3.64406 ( 3240) SS BOND : bond 0.00495 ( 36) SS BOND : angle 1.36947 ( 72) covalent geometry : bond 0.00498 (19512) covalent geometry : angle 0.56027 (25836) Misc. bond : bond 0.00039 ( 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 368 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 342 time to evaluate : 2.088 Fit side-chains REVERT: D 34 ARG cc_start: 0.8886 (mtt180) cc_final: 0.8680 (mtt180) REVERT: F 257 MET cc_start: 0.9113 (mmt) cc_final: 0.8683 (mmt) REVERT: L 257 MET cc_start: 0.9099 (mmt) cc_final: 0.8832 (mmt) outliers start: 26 outliers final: 15 residues processed: 351 average time/residue: 0.3528 time to fit residues: 190.8497 Evaluate side-chains 347 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 27 LEU 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 112 optimal weight: 0.4980 chunk 189 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.146022 restraints weight = 16967.081| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.45 r_work: 0.3334 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1796 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= 0.107 Angle : 0.439 4.625 25908 Z= 0.235 Chirality : 0.040 0.139 2844 Planarity : 0.003 0.021 3024 Dihedral : 12.958 59.974 3708 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.33 % Allowed : 7.00 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.17), residues: 2124 helix: 2.29 (0.14), residues: 1392 sheet: 1.40 (0.43), residues: 144 loop : -0.28 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.002 0.000 HIS D 75 PHE 0.006 0.001 PHE G 198 TYR 0.012 0.001 TYR A 67 ARG 0.001 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 1104) hydrogen bonds : angle 3.45070 ( 3240) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.96429 ( 72) covalent geometry : bond 0.00237 (19512) covalent geometry : angle 0.43662 (25836) Misc. bond : bond 0.00004 ( 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 378 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 2.219 Fit side-chains REVERT: D 34 ARG cc_start: 0.8851 (mtt180) cc_final: 0.8647 (mtt180) REVERT: F 257 MET cc_start: 0.9128 (mmt) cc_final: 0.8720 (mmt) outliers start: 26 outliers final: 15 residues processed: 364 average time/residue: 0.3990 time to fit residues: 224.5697 Evaluate side-chains 357 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 342 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 167 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.153642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.146889 restraints weight = 17017.294| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.44 r_work: 0.3353 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19560 Z= 0.105 Angle : 0.431 4.603 25908 Z= 0.231 Chirality : 0.040 0.142 2844 Planarity : 0.003 0.021 3024 Dihedral : 12.310 59.969 3708 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.23 % Allowed : 8.74 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.17), residues: 2124 helix: 2.56 (0.13), residues: 1452 sheet: 1.42 (0.43), residues: 144 loop : -0.05 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 79 HIS 0.002 0.000 HIS G 75 PHE 0.005 0.001 PHE E 198 TYR 0.011 0.001 TYR J 67 ARG 0.001 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1104) hydrogen bonds : angle 3.36029 ( 3240) SS BOND : bond 0.00206 ( 36) SS BOND : angle 0.87985 ( 72) covalent geometry : bond 0.00236 (19512) covalent geometry : angle 0.42958 (25836) Misc. bond : bond 0.00004 ( 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 378 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 354 time to evaluate : 2.008 Fit side-chains REVERT: D 34 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8602 (mtt180) REVERT: F 257 MET cc_start: 0.9130 (mmt) cc_final: 0.8709 (mmt) outliers start: 24 outliers final: 16 residues processed: 361 average time/residue: 0.2988 time to fit residues: 167.4699 Evaluate side-chains 358 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 342 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.151870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.145067 restraints weight = 17053.151| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.44 r_work: 0.3333 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19560 Z= 0.132 Angle : 0.468 4.626 25908 Z= 0.247 Chirality : 0.042 0.147 2844 Planarity : 0.003 0.023 3024 Dihedral : 12.244 59.987 3708 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.28 % Allowed : 9.61 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.17), residues: 2124 helix: 2.55 (0.13), residues: 1452 sheet: 1.37 (0.43), residues: 144 loop : -0.06 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 79 HIS 0.002 0.000 HIS G 75 PHE 0.006 0.001 PHE C 71 TYR 0.014 0.002 TYR H 67 ARG 0.001 0.000 ARG L 206 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 1104) hydrogen bonds : angle 3.38764 ( 3240) SS BOND : bond 0.00300 ( 36) SS BOND : angle 1.05908 ( 72) covalent geometry : bond 0.00316 (19512) covalent geometry : angle 0.46489 (25836) Misc. bond : bond 0.00012 ( 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 375 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 350 time to evaluate : 1.948 Fit side-chains REVERT: C 3 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7417 (mm-30) REVERT: D 34 ARG cc_start: 0.8833 (mtt180) cc_final: 0.8616 (mtt180) outliers start: 25 outliers final: 16 residues processed: 358 average time/residue: 0.3139 time to fit residues: 174.6599 Evaluate side-chains 358 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 342 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 132 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.154093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.115714 restraints weight = 16920.887| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.47 r_work: 0.2632 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2133 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 : 0.415 4.602 25908 Z= 0.222 Chirality : 0.039 0.137 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.713 59.944 3708 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.18 % Allowed : 10.02 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2124 helix: 2.76 (0.13), residues: 1452 sheet: 1.54 (0.44), residues: 144 loop : 0.01 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.000 HIS D 75 PHE 0.005 0.001 PHE G 53 TYR 0.009 0.001 TYR G 67 ARG 0.001 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1104) hydrogen bonds : angle 3.29938 ( 3240) SS BOND : bond 0.00169 ( 36) SS BOND : angle 0.86655 ( 72) covalent geometry : bond 0.00206 (19512) covalent geometry : angle 0.41308 (25836) Misc. bond : bond 0.00001 ( 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 374 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 351 time to evaluate : 2.752 Fit side-chains REVERT: C 3 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: D 34 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8532 (mtt180) REVERT: E 230 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 23 outliers final: 17 residues processed: 357 average time/residue: 0.3202 time to fit residues: 180.5448 Evaluate side-chains 361 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 343 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 3 GLU 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 G residue 44 THR Chi-restraints excluded: chain G residue 269 LEU 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 163 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.149645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.142758 restraints weight = 17018.798| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.45 r_work: 0.3307 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19560 Z= 0.187 Angle : 0.538 4.716 25908 Z= 0.281 Chirality : 0.045 0.160 2844 Planarity : 0.004 0.037 3024 Dihedral : 12.398 59.959 3708 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.07 % Allowed : 10.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.17), residues: 2124 helix: 2.44 (0.13), residues: 1452 sheet: -0.11 (0.38), residues: 204 loop : -0.10 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 79 HIS 0.002 0.000 HIS G 75 PHE 0.008 0.001 PHE F 71 TYR 0.017 0.002 TYR E 67 ARG 0.002 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.05863 ( 1104) hydrogen bonds : angle 3.49445 ( 3240) SS BOND : bond 0.00465 ( 36) SS BOND : angle 1.31488 ( 72) covalent geometry : bond 0.00464 (19512) covalent geometry : angle 0.53395 (25836) Misc. bond : bond 0.00026 ( 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 369 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 348 time to evaluate : 2.202 Fit side-chains REVERT: D 34 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8568 (mtt180) outliers start: 21 outliers final: 17 residues processed: 351 average time/residue: 0.3074 time to fit residues: 166.6664 Evaluate side-chains 363 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 346 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 G residue 44 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I 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 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 119 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 146 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.152672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.113310 restraints weight = 17012.312| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.59 r_work: 0.2634 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19560 Z= 0.108 Angle : 0.436 4.606 25908 Z= 0.233 Chirality : 0.040 0.140 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.744 59.529 3708 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.97 % Allowed : 10.74 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.17), residues: 2124 helix: 2.59 (0.13), residues: 1464 sheet: 1.60 (0.45), residues: 144 loop : -0.14 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.003 0.000 HIS D 75 PHE 0.005 0.001 PHE G 53 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 1104) hydrogen bonds : angle 3.34948 ( 3240) SS BOND : bond 0.00214 ( 36) SS BOND : angle 0.93551 ( 72) covalent geometry : bond 0.00245 (19512) covalent geometry : angle 0.43411 (25836) Misc. bond : bond 0.00002 ( 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 369 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 350 time to evaluate : 2.109 Fit side-chains REVERT: D 34 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8530 (mtt180) outliers start: 19 outliers final: 15 residues processed: 352 average time/residue: 0.2987 time to fit residues: 162.9690 Evaluate side-chains 364 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 349 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 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 171 optimal weight: 0.4980 chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.0010 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.151848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.145029 restraints weight = 16950.916| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.43 r_work: 0.3336 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19560 Z= 0.131 Angle : 0.465 4.628 25908 Z= 0.247 Chirality : 0.041 0.147 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.695 59.042 3708 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.17), residues: 2124 helix: 2.64 (0.13), residues: 1452 sheet: 1.66 (0.46), residues: 144 loop : -0.06 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.002 0.000 HIS G 75 PHE 0.006 0.001 PHE C 71 TYR 0.014 0.002 TYR A 67 ARG 0.001 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 1104) hydrogen bonds : angle 3.37560 ( 3240) SS BOND : bond 0.00299 ( 36) SS BOND : angle 0.99246 ( 72) covalent geometry : bond 0.00312 (19512) covalent geometry : angle 0.46300 (25836) Misc. bond : bond 0.00015 ( 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 368 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 352 time to evaluate : 1.910 Fit side-chains REVERT: D 34 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8556 (mtt180) outliers start: 16 outliers final: 16 residues processed: 353 average time/residue: 0.2984 time to fit residues: 162.3437 Evaluate side-chains 365 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 349 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 G residue 44 THR Chi-restraints excluded: chain I 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 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 93 optimal weight: 0.3980 chunk 202 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 113 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.154009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.112101 restraints weight = 173129.710| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 7.39 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2316 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= 0.097 Angle : 0.413 4.599 25908 Z= 0.222 Chirality : 0.040 0.136 2844 Planarity : 0.003 0.021 3024 Dihedral : 11.049 59.040 3708 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.87 % Allowed : 10.99 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.18), residues: 2124 helix: 2.77 (0.13), residues: 1464 sheet: 1.81 (0.46), residues: 144 loop : -0.07 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.002 0.000 HIS G 75 PHE 0.005 0.001 PHE G 198 TYR 0.009 0.001 TYR G 67 ARG 0.001 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 1104) hydrogen bonds : angle 3.26729 ( 3240) SS BOND : bond 0.00162 ( 36) SS BOND : angle 0.83389 ( 72) covalent geometry : bond 0.00214 (19512) covalent geometry : angle 0.41166 (25836) Misc. bond : bond 0.00003 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8997.65 seconds wall clock time: 159 minutes 26.04 seconds (9566.04 seconds total)