Starting phenix.real_space_refine on Tue Aug 26 09:53:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgd_38318/08_2025/8xgd_38318_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 12360 2.51 5 N 2784 2.21 5 O 3036 1.98 5 H 17316 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35652 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2886 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "E" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2886 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'MC3': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'MC3:plan-1': 5, 'MC3:plan-2': 5} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'MC3': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'MC3:plan-1': 5, 'MC3:plan-2': 5} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: B, C, D, G, H, I, J, K, F, L Time building chain proxies: 5.53, per 1000 atoms: 0.16 Number of scatterers: 35652 At special positions: 0 Unit cell: (102.582, 97.578, 139.278, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 3036 8.00 N 2784 7.00 C 12360 6.00 H 17316 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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 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 B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 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 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 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=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 937.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 74.9% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 221 Processing helix chain 'A' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 removed outlier: 4.237A pdb=" N LEU F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 34 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.187A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 221 Processing helix chain 'F' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.253A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.237A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 221 Processing helix chain 'C' and resid 246 through 276 removed outlier: 3.595A pdb=" N LYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 221 Processing helix chain 'D' and resid 246 through 276 removed outlier: 3.595A pdb=" N LYS D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.237A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 221 Processing helix chain 'E' and resid 246 through 276 removed outlier: 3.595A pdb=" N LYS E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.237A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 34 Processing helix chain 'H' and resid 34 through 41 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.954A 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 97 removed outlier: 4.254A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 221 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.595A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 34 through 41 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 15 removed outlier: 4.237A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 34 through 41 Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.956A 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 97 removed outlier: 4.255A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 34 through 41 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.954A 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 97 removed outlier: 4.254A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.595A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 4.238A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 34 through 41 Processing helix chain 'L' and resid 41 through 46 removed outlier: 4.188A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.955A 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 97 removed outlier: 4.254A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.594A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.599A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.599A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.600A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3420 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: 8.30 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17280 1.04 - 1.23: 332 1.23 - 1.43: 7360 1.43 - 1.62: 10872 1.62 - 1.82: 204 Bond restraints: 36048 Sorted by residual: bond pdb=" CAJ Y01 A 404 " pdb=" CAO Y01 A 404 " ideal model delta sigma weight residual 1.526 1.458 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CAJ Y01 D 404 " pdb=" CAO Y01 D 404 " ideal model delta sigma weight residual 1.526 1.458 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CAJ Y01 B 404 " pdb=" CAO Y01 B 404 " ideal model delta sigma weight residual 1.526 1.458 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CAJ Y01 E 406 " pdb=" CAO Y01 E 406 " ideal model delta sigma weight residual 1.526 1.458 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CAJ Y01 J 404 " pdb=" CAO Y01 J 404 " ideal model delta sigma weight residual 1.526 1.458 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 36043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 63913 2.46 - 4.93: 347 4.93 - 7.39: 36 7.39 - 9.86: 24 9.86 - 12.32: 48 Bond angle restraints: 64368 Sorted by residual: angle pdb=" CAC Y01 C 404 " pdb=" CBB Y01 C 404 " pdb=" CBE Y01 C 404 " ideal model delta sigma weight residual 113.31 125.63 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CAC Y01 K 404 " pdb=" CBB Y01 K 404 " pdb=" CBE Y01 K 404 " ideal model delta sigma weight residual 113.31 125.62 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" CAC Y01 G 404 " pdb=" CBB Y01 G 404 " pdb=" CBE Y01 G 404 " ideal model delta sigma weight residual 113.31 125.61 -12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" CAC Y01 B 404 " pdb=" CBB Y01 B 404 " pdb=" CBE Y01 B 404 " ideal model delta sigma weight residual 113.31 125.61 -12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" CAC Y01 E 406 " pdb=" CBB Y01 E 406 " pdb=" CBE Y01 E 406 " ideal model delta sigma weight residual 113.31 125.61 -12.30 3.00e+00 1.11e-01 1.68e+01 ... (remaining 64363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 16107 14.63 - 29.26: 1269 29.26 - 43.89: 270 43.89 - 58.51: 216 58.51 - 73.14: 12 Dihedral angle restraints: 17874 sinusoidal: 10026 harmonic: 7848 Sorted by residual: dihedral pdb=" CA LYS C 238 " pdb=" CB LYS C 238 " pdb=" CG LYS C 238 " pdb=" CD LYS C 238 " ideal model delta sinusoidal sigma weight residual 60.00 107.67 -47.67 3 1.50e+01 4.44e-03 8.53e+00 dihedral pdb=" CA LYS F 238 " pdb=" CB LYS F 238 " pdb=" CG LYS F 238 " pdb=" CD LYS F 238 " ideal model delta sinusoidal sigma weight residual 60.00 107.66 -47.66 3 1.50e+01 4.44e-03 8.53e+00 dihedral pdb=" CA LYS L 238 " pdb=" CB LYS L 238 " pdb=" CG LYS L 238 " pdb=" CD LYS L 238 " ideal model delta sinusoidal sigma weight residual 60.00 107.66 -47.66 3 1.50e+01 4.44e-03 8.53e+00 ... (remaining 17871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1714 0.029 - 0.059: 791 0.059 - 0.088: 304 0.088 - 0.117: 87 0.117 - 0.147: 20 Chirality restraints: 2916 Sorted by residual: chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE H 73 " pdb=" N ILE H 73 " pdb=" C ILE H 73 " pdb=" CB ILE H 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE K 73 " pdb=" N ILE K 73 " pdb=" C ILE K 73 " pdb=" CB ILE K 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2913 not shown) Planarity restraints: 5064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU J 249 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLU J 249 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU J 249 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS J 250 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 249 " 0.021 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C GLU C 249 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU C 249 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 250 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 249 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLU E 249 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU E 249 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS E 250 " -0.024 2.00e-02 2.50e+03 ... (remaining 5061 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 7773 2.33 - 2.90: 76728 2.90 - 3.46: 84748 3.46 - 4.03: 117989 4.03 - 4.60: 183328 Nonbonded interactions: 470566 Sorted by model distance: nonbonded pdb=" OE1 GLU F 230 " pdb=" HZ1 LYS G 238 " model vdw 1.761 2.450 nonbonded pdb=" OE1 GLU A 230 " pdb=" HZ1 LYS L 238 " model vdw 1.765 2.450 nonbonded pdb=" OE1 GLU B 230 " pdb=" HZ1 LYS K 238 " model vdw 1.765 2.450 nonbonded pdb=" HZ1 LYS C 238 " pdb=" OE1 GLU J 230 " model vdw 1.766 2.450 nonbonded pdb=" OE1 GLU E 230 " pdb=" HZ1 LYS H 238 " model vdw 1.766 2.450 ... (remaining 470561 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'B' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'C' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'D' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 276 or (resid 401 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 402 and (name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40)) or resid 403 or resid 405)) selection = (chain 'F' and (resid 2 through 276 or (resid 401 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 402 and (name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40)) or resid 403 or resid 405)) selection = (chain 'G' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'H' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'I' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'J' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'K' and (resid 2 through 402 or (resid 403 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 405 and (name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'L' and (resid 2 through 276 or (resid 401 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44) \ ) or (resid 402 and (name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40)) or resid 403 or resid 405)) } 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: 1.800 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: 0.210 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.360 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.004 0.068 18762 Z= 0.223 Angle : 0.894 12.321 25356 Z= 0.401 Chirality : 0.040 0.147 2916 Planarity : 0.007 0.053 3012 Dihedral : 11.980 73.143 7512 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.17), residues: 2100 helix: 0.49 (0.13), residues: 1380 sheet: 1.33 (0.48), residues: 144 loop : -1.52 (0.20), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 24 TYR 0.013 0.002 TYR E 67 PHE 0.015 0.002 PHE D 205 TRP 0.008 0.001 TRP F 79 HIS 0.004 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (18732) covalent geometry : angle 0.89311 (25296) SS BOND : bond 0.00429 ( 30) SS BOND : angle 1.13601 ( 60) hydrogen bonds : bond 0.14407 ( 1152) hydrogen bonds : angle 5.51106 ( 3420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 366 average time/residue: 1.2899 time to fit residues: 531.2102 Evaluate side-chains 245 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 241 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain K residue 263 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 232 ASN F 63 ASN G 16 GLN G 63 ASN G 232 ASN B 16 GLN B 63 ASN B 232 ASN C 63 ASN D 63 ASN D 232 ASN E 16 GLN E 63 ASN E 232 ASN H 63 ASN I 63 ASN I 232 ASN J 16 GLN J 63 ASN J 232 ASN K 63 ASN L 63 ASN L 232 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.210910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170008 restraints weight = 47683.725| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.10 r_work: 0.3735 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18762 Z= 0.188 Angle : 0.633 5.089 25356 Z= 0.338 Chirality : 0.043 0.148 2916 Planarity : 0.006 0.043 3012 Dihedral : 10.514 54.096 3632 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.40 % Allowed : 8.64 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2100 helix: 1.67 (0.13), residues: 1440 sheet: 1.51 (0.46), residues: 144 loop : -1.57 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 69 TYR 0.017 0.003 TYR K 67 PHE 0.011 0.002 PHE C 253 TRP 0.008 0.002 TRP K 79 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00411 (18732) covalent geometry : angle 0.62970 (25296) SS BOND : bond 0.00757 ( 30) SS BOND : angle 1.42387 ( 60) hydrogen bonds : bond 0.07243 ( 1152) hydrogen bonds : angle 4.22418 ( 3420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6622 (t0) cc_final: 0.6031 (m-40) REVERT: F 273 ASN cc_start: 0.6828 (t0) cc_final: 0.6224 (m-40) REVERT: G 273 ASN cc_start: 0.6646 (t0) cc_final: 0.6118 (m-40) REVERT: B 273 ASN cc_start: 0.6620 (t0) cc_final: 0.6098 (m110) REVERT: C 273 ASN cc_start: 0.6801 (t0) cc_final: 0.6196 (m-40) REVERT: D 273 ASN cc_start: 0.6604 (t0) cc_final: 0.6025 (m-40) REVERT: E 273 ASN cc_start: 0.6617 (t0) cc_final: 0.6112 (m110) REVERT: H 273 ASN cc_start: 0.6812 (t0) cc_final: 0.6207 (m-40) REVERT: I 273 ASN cc_start: 0.6620 (t0) cc_final: 0.6037 (m-40) REVERT: J 273 ASN cc_start: 0.6660 (t0) cc_final: 0.6122 (m-40) REVERT: K 273 ASN cc_start: 0.6819 (t0) cc_final: 0.6209 (m-40) REVERT: L 273 ASN cc_start: 0.6614 (t0) cc_final: 0.6024 (m-40) outliers start: 27 outliers final: 24 residues processed: 264 average time/residue: 1.0509 time to fit residues: 319.0884 Evaluate side-chains 253 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 263 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN B 16 GLN E 16 GLN J 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.207570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168623 restraints weight = 48477.569| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.19 r_work: 0.3685 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18762 Z= 0.182 Angle : 0.634 4.809 25356 Z= 0.333 Chirality : 0.042 0.147 2916 Planarity : 0.005 0.038 3012 Dihedral : 8.974 40.838 3632 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.43 % Allowed : 9.68 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2100 helix: 1.93 (0.13), residues: 1440 sheet: 1.19 (0.43), residues: 144 loop : -1.51 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 69 TYR 0.017 0.003 TYR K 67 PHE 0.011 0.002 PHE L 253 TRP 0.006 0.002 TRP F 79 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00407 (18732) covalent geometry : angle 0.63035 (25296) SS BOND : bond 0.00802 ( 30) SS BOND : angle 1.49106 ( 60) hydrogen bonds : bond 0.07109 ( 1152) hydrogen bonds : angle 4.14869 ( 3420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASN cc_start: 0.8064 (m110) cc_final: 0.7836 (m110) REVERT: A 273 ASN cc_start: 0.6857 (t0) cc_final: 0.6283 (m-40) REVERT: F 273 ASN cc_start: 0.6947 (t0) cc_final: 0.6321 (m-40) REVERT: G 273 ASN cc_start: 0.6828 (t0) cc_final: 0.6317 (m-40) REVERT: B 273 ASN cc_start: 0.6800 (t0) cc_final: 0.6292 (m-40) REVERT: C 273 ASN cc_start: 0.6973 (t0) cc_final: 0.6342 (m-40) REVERT: D 207 ASN cc_start: 0.8045 (m110) cc_final: 0.7807 (m110) REVERT: D 273 ASN cc_start: 0.6859 (t0) cc_final: 0.6305 (m-40) REVERT: E 273 ASN cc_start: 0.6791 (t0) cc_final: 0.6287 (m-40) REVERT: H 273 ASN cc_start: 0.6923 (t0) cc_final: 0.6307 (m-40) REVERT: I 207 ASN cc_start: 0.8052 (m110) cc_final: 0.7816 (m110) REVERT: I 273 ASN cc_start: 0.6874 (t0) cc_final: 0.6303 (m-40) REVERT: J 273 ASN cc_start: 0.6825 (t0) cc_final: 0.6295 (m-40) REVERT: K 273 ASN cc_start: 0.6951 (t0) cc_final: 0.6335 (m-40) REVERT: L 207 ASN cc_start: 0.8048 (m110) cc_final: 0.7814 (m110) REVERT: L 273 ASN cc_start: 0.6854 (t0) cc_final: 0.6282 (m-40) outliers start: 47 outliers final: 32 residues processed: 279 average time/residue: 1.0485 time to fit residues: 335.6461 Evaluate side-chains 267 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN B 16 GLN E 16 GLN J 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.205104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166735 restraints weight = 48205.871| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.17 r_work: 0.3655 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18762 Z= 0.227 Angle : 0.697 5.416 25356 Z= 0.370 Chirality : 0.044 0.157 2916 Planarity : 0.006 0.051 3012 Dihedral : 9.214 47.216 3632 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.80 % Allowed : 10.30 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.17), residues: 2100 helix: 1.76 (0.13), residues: 1368 sheet: 0.98 (0.42), residues: 144 loop : -1.65 (0.18), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 69 TYR 0.021 0.004 TYR H 67 PHE 0.013 0.002 PHE L 253 TRP 0.008 0.002 TRP L 79 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00524 (18732) covalent geometry : angle 0.69119 (25296) SS BOND : bond 0.01002 ( 30) SS BOND : angle 1.90101 ( 60) hydrogen bonds : bond 0.07791 ( 1152) hydrogen bonds : angle 4.20472 ( 3420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6957 (t0) cc_final: 0.6393 (m-40) REVERT: F 273 ASN cc_start: 0.7088 (t0) cc_final: 0.6522 (m-40) REVERT: G 239 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: G 273 ASN cc_start: 0.7044 (t0) cc_final: 0.6546 (m-40) REVERT: B 273 ASN cc_start: 0.6977 (t0) cc_final: 0.6486 (m-40) REVERT: C 273 ASN cc_start: 0.7035 (t0) cc_final: 0.6472 (m-40) REVERT: D 238 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7853 (mtpt) REVERT: D 273 ASN cc_start: 0.6942 (t0) cc_final: 0.6395 (m-40) REVERT: E 239 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: E 273 ASN cc_start: 0.6960 (t0) cc_final: 0.6483 (m-40) REVERT: H 273 ASN cc_start: 0.6979 (t0) cc_final: 0.6432 (m-40) REVERT: I 273 ASN cc_start: 0.6934 (t0) cc_final: 0.6397 (m-40) REVERT: J 239 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: J 273 ASN cc_start: 0.6995 (t0) cc_final: 0.6485 (m-40) REVERT: K 273 ASN cc_start: 0.7001 (t0) cc_final: 0.6455 (m-40) REVERT: L 273 ASN cc_start: 0.6957 (t0) cc_final: 0.6395 (m-40) outliers start: 54 outliers final: 33 residues processed: 290 average time/residue: 1.0477 time to fit residues: 348.6859 Evaluate side-chains 277 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN B 16 GLN E 16 GLN J 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.207312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169120 restraints weight = 48262.217| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.17 r_work: 0.3686 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18762 Z= 0.148 Angle : 0.585 4.771 25356 Z= 0.309 Chirality : 0.040 0.131 2916 Planarity : 0.004 0.035 3012 Dihedral : 8.195 43.270 3624 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.02 % Allowed : 11.23 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2100 helix: 2.09 (0.13), residues: 1440 sheet: 0.92 (0.40), residues: 144 loop : -1.41 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 69 TYR 0.015 0.002 TYR K 67 PHE 0.011 0.002 PHE B 93 TRP 0.005 0.001 TRP A 79 HIS 0.005 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00321 (18732) covalent geometry : angle 0.58271 (25296) SS BOND : bond 0.00545 ( 30) SS BOND : angle 1.27323 ( 60) hydrogen bonds : bond 0.06457 ( 1152) hydrogen bonds : angle 4.06636 ( 3420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7747 (mtpt) REVERT: A 273 ASN cc_start: 0.6931 (t0) cc_final: 0.6348 (m-40) REVERT: F 273 ASN cc_start: 0.6984 (t0) cc_final: 0.6402 (m-40) REVERT: G 273 ASN cc_start: 0.6911 (t0) cc_final: 0.6379 (m-40) REVERT: B 273 ASN cc_start: 0.6867 (t0) cc_final: 0.6336 (m-40) REVERT: C 273 ASN cc_start: 0.6976 (t0) cc_final: 0.6400 (m-40) REVERT: D 273 ASN cc_start: 0.6916 (t0) cc_final: 0.6350 (m-40) REVERT: E 273 ASN cc_start: 0.6862 (t0) cc_final: 0.6344 (m-40) REVERT: H 273 ASN cc_start: 0.6942 (t0) cc_final: 0.6378 (m-40) REVERT: I 273 ASN cc_start: 0.6922 (t0) cc_final: 0.6359 (m-40) REVERT: J 273 ASN cc_start: 0.6898 (t0) cc_final: 0.6348 (m-40) REVERT: K 273 ASN cc_start: 0.6948 (t0) cc_final: 0.6398 (m-40) REVERT: L 273 ASN cc_start: 0.6933 (t0) cc_final: 0.6355 (m-40) outliers start: 39 outliers final: 32 residues processed: 258 average time/residue: 1.1352 time to fit residues: 335.1861 Evaluate side-chains 257 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 191 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.0070 chunk 52 optimal weight: 10.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN B 16 GLN E 16 GLN J 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.211621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171806 restraints weight = 47838.491| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.10 r_work: 0.3747 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18762 Z= 0.110 Angle : 0.500 4.984 25356 Z= 0.263 Chirality : 0.037 0.119 2916 Planarity : 0.003 0.023 3012 Dihedral : 6.802 48.427 3624 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.19 % Allowed : 11.85 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.17), residues: 2100 helix: 2.70 (0.13), residues: 1440 sheet: 1.99 (0.40), residues: 120 loop : -1.53 (0.20), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 24 TYR 0.011 0.002 TYR K 243 PHE 0.012 0.001 PHE G 93 TRP 0.002 0.001 TRP K 79 HIS 0.004 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00222 (18732) covalent geometry : angle 0.49892 (25296) SS BOND : bond 0.00221 ( 30) SS BOND : angle 0.86472 ( 60) hydrogen bonds : bond 0.05043 ( 1152) hydrogen bonds : angle 3.87853 ( 3420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6641 (t0) cc_final: 0.6031 (m-40) REVERT: F 273 ASN cc_start: 0.6785 (t0) cc_final: 0.6183 (m-40) REVERT: G 273 ASN cc_start: 0.6559 (t0) cc_final: 0.6045 (m-40) REVERT: B 273 ASN cc_start: 0.6590 (t0) cc_final: 0.6047 (m-40) REVERT: C 273 ASN cc_start: 0.6770 (t0) cc_final: 0.6181 (m-40) REVERT: D 273 ASN cc_start: 0.6642 (t0) cc_final: 0.6032 (m-40) REVERT: E 273 ASN cc_start: 0.6560 (t0) cc_final: 0.6033 (m-40) REVERT: H 273 ASN cc_start: 0.6782 (t0) cc_final: 0.6186 (m-40) REVERT: I 273 ASN cc_start: 0.6620 (t0) cc_final: 0.6002 (m-40) REVERT: J 273 ASN cc_start: 0.6554 (t0) cc_final: 0.6036 (m-40) REVERT: K 273 ASN cc_start: 0.6777 (t0) cc_final: 0.6197 (m-40) REVERT: L 273 ASN cc_start: 0.6639 (t0) cc_final: 0.6025 (m-40) outliers start: 23 outliers final: 17 residues processed: 229 average time/residue: 1.1816 time to fit residues: 309.5932 Evaluate side-chains 224 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 176 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN E 16 GLN J 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.205907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168627 restraints weight = 48111.626| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.16 r_work: 0.3674 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18762 Z= 0.196 Angle : 0.644 5.228 25356 Z= 0.340 Chirality : 0.042 0.150 2916 Planarity : 0.005 0.041 3012 Dihedral : 8.137 50.502 3624 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.28 % Allowed : 10.87 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.17), residues: 2100 helix: 2.30 (0.13), residues: 1440 sheet: 0.93 (0.40), residues: 144 loop : -1.25 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 24 TYR 0.017 0.003 TYR K 67 PHE 0.012 0.002 PHE J 71 TRP 0.007 0.002 TRP K 79 HIS 0.005 0.002 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (18732) covalent geometry : angle 0.64003 (25296) SS BOND : bond 0.00868 ( 30) SS BOND : angle 1.59638 ( 60) hydrogen bonds : bond 0.06878 ( 1152) hydrogen bonds : angle 4.01834 ( 3420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6912 (t0) cc_final: 0.6342 (m-40) REVERT: F 273 ASN cc_start: 0.6949 (t0) cc_final: 0.6390 (m-40) REVERT: G 273 ASN cc_start: 0.6788 (t0) cc_final: 0.6268 (m-40) REVERT: B 273 ASN cc_start: 0.6759 (t0) cc_final: 0.6242 (m-40) REVERT: C 273 ASN cc_start: 0.6948 (t0) cc_final: 0.6379 (m-40) REVERT: D 273 ASN cc_start: 0.6909 (t0) cc_final: 0.6351 (m-40) REVERT: E 273 ASN cc_start: 0.6749 (t0) cc_final: 0.6229 (m-40) REVERT: H 273 ASN cc_start: 0.6899 (t0) cc_final: 0.6340 (m-40) REVERT: I 273 ASN cc_start: 0.6899 (t0) cc_final: 0.6345 (m-40) REVERT: J 273 ASN cc_start: 0.6782 (t0) cc_final: 0.6244 (m-40) REVERT: K 273 ASN cc_start: 0.6912 (t0) cc_final: 0.6362 (m-40) REVERT: L 273 ASN cc_start: 0.6908 (t0) cc_final: 0.6338 (m-40) outliers start: 44 outliers final: 30 residues processed: 253 average time/residue: 1.1570 time to fit residues: 337.3104 Evaluate side-chains 248 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.207239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169182 restraints weight = 48156.619| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.19 r_work: 0.3694 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18762 Z= 0.144 Angle : 0.572 4.776 25356 Z= 0.301 Chirality : 0.040 0.133 2916 Planarity : 0.004 0.033 3012 Dihedral : 7.860 52.581 3624 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.92 % Allowed : 11.65 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.17), residues: 2100 helix: 2.48 (0.13), residues: 1440 sheet: 0.99 (0.39), residues: 144 loop : -1.27 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.014 0.002 TYR K 67 PHE 0.010 0.002 PHE E 93 TRP 0.005 0.001 TRP H 79 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00313 (18732) covalent geometry : angle 0.56885 (25296) SS BOND : bond 0.00544 ( 30) SS BOND : angle 1.26818 ( 60) hydrogen bonds : bond 0.06088 ( 1152) hydrogen bonds : angle 3.94123 ( 3420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6867 (t0) cc_final: 0.6283 (m-40) REVERT: F 273 ASN cc_start: 0.6884 (t0) cc_final: 0.6296 (m-40) REVERT: G 273 ASN cc_start: 0.6739 (t0) cc_final: 0.6208 (m-40) REVERT: B 273 ASN cc_start: 0.6703 (t0) cc_final: 0.6167 (m-40) REVERT: C 273 ASN cc_start: 0.6890 (t0) cc_final: 0.6302 (m-40) REVERT: D 273 ASN cc_start: 0.6790 (t0) cc_final: 0.6209 (m-40) REVERT: E 273 ASN cc_start: 0.6700 (t0) cc_final: 0.6181 (m-40) REVERT: H 273 ASN cc_start: 0.6855 (t0) cc_final: 0.6280 (m-40) REVERT: I 273 ASN cc_start: 0.6782 (t0) cc_final: 0.6204 (m-40) REVERT: J 273 ASN cc_start: 0.6707 (t0) cc_final: 0.6167 (m-40) REVERT: K 273 ASN cc_start: 0.6868 (t0) cc_final: 0.6299 (m-40) REVERT: L 273 ASN cc_start: 0.6795 (t0) cc_final: 0.6203 (m-40) outliers start: 37 outliers final: 34 residues processed: 247 average time/residue: 1.1489 time to fit residues: 327.2218 Evaluate side-chains 251 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.5324 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.206834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168878 restraints weight = 48027.293| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.16 r_work: 0.3690 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18762 Z= 0.152 Angle : 0.585 5.212 25356 Z= 0.307 Chirality : 0.040 0.135 2916 Planarity : 0.005 0.057 3012 Dihedral : 7.931 57.195 3624 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.07 % Allowed : 11.75 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.17), residues: 2100 helix: 2.48 (0.13), residues: 1440 sheet: 1.02 (0.40), residues: 144 loop : -1.23 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 24 TYR 0.014 0.002 TYR H 67 PHE 0.010 0.002 PHE E 93 TRP 0.005 0.001 TRP F 79 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (18732) covalent geometry : angle 0.58199 (25296) SS BOND : bond 0.00608 ( 30) SS BOND : angle 1.30827 ( 60) hydrogen bonds : bond 0.06182 ( 1152) hydrogen bonds : angle 3.92708 ( 3420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6903 (t0) cc_final: 0.6336 (m-40) REVERT: F 273 ASN cc_start: 0.6922 (t0) cc_final: 0.6361 (m-40) REVERT: G 273 ASN cc_start: 0.6769 (t0) cc_final: 0.6254 (m-40) REVERT: B 273 ASN cc_start: 0.6744 (t0) cc_final: 0.6219 (m-40) REVERT: C 273 ASN cc_start: 0.6910 (t0) cc_final: 0.6362 (m-40) REVERT: D 273 ASN cc_start: 0.6823 (t0) cc_final: 0.6258 (m-40) REVERT: E 273 ASN cc_start: 0.6726 (t0) cc_final: 0.6216 (m-40) REVERT: H 273 ASN cc_start: 0.6875 (t0) cc_final: 0.6337 (m-40) REVERT: I 273 ASN cc_start: 0.6813 (t0) cc_final: 0.6245 (m-40) REVERT: J 273 ASN cc_start: 0.6751 (t0) cc_final: 0.6222 (m-40) REVERT: K 273 ASN cc_start: 0.6885 (t0) cc_final: 0.6348 (m-40) REVERT: L 273 ASN cc_start: 0.6825 (t0) cc_final: 0.6249 (m-40) outliers start: 40 outliers final: 33 residues processed: 252 average time/residue: 1.1576 time to fit residues: 336.3106 Evaluate side-chains 253 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN B 16 GLN J 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.203186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165000 restraints weight = 48024.922| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.24 r_work: 0.3637 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18762 Z= 0.270 Angle : 0.754 6.075 25356 Z= 0.404 Chirality : 0.047 0.168 2916 Planarity : 0.006 0.057 3012 Dihedral : 9.542 59.752 3624 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.23 % Allowed : 11.65 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.17), residues: 2100 helix: 1.76 (0.13), residues: 1440 sheet: 0.88 (0.40), residues: 144 loop : -1.23 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 24 TYR 0.023 0.004 TYR C 67 PHE 0.016 0.003 PHE K 253 TRP 0.011 0.003 TRP A 79 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00645 (18732) covalent geometry : angle 0.74824 (25296) SS BOND : bond 0.01200 ( 30) SS BOND : angle 2.10703 ( 60) hydrogen bonds : bond 0.08137 ( 1152) hydrogen bonds : angle 4.21123 ( 3420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.6976 (t0) cc_final: 0.6389 (m-40) REVERT: F 273 ASN cc_start: 0.7002 (t0) cc_final: 0.6434 (m-40) REVERT: G 273 ASN cc_start: 0.6992 (t0) cc_final: 0.6498 (m-40) REVERT: B 273 ASN cc_start: 0.6911 (t0) cc_final: 0.6409 (m-40) REVERT: C 273 ASN cc_start: 0.7032 (t0) cc_final: 0.6465 (m-40) REVERT: D 273 ASN cc_start: 0.6962 (t0) cc_final: 0.6390 (m-40) REVERT: E 239 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: E 273 ASN cc_start: 0.6888 (t0) cc_final: 0.6404 (m-40) REVERT: H 273 ASN cc_start: 0.6977 (t0) cc_final: 0.6417 (m-40) REVERT: I 273 ASN cc_start: 0.6938 (t0) cc_final: 0.6374 (m-40) REVERT: J 239 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: J 273 ASN cc_start: 0.6909 (t0) cc_final: 0.6407 (m-40) REVERT: K 273 ASN cc_start: 0.6979 (t0) cc_final: 0.6429 (m-40) REVERT: L 273 ASN cc_start: 0.6957 (t0) cc_final: 0.6376 (m-40) outliers start: 43 outliers final: 39 residues processed: 263 average time/residue: 1.0770 time to fit residues: 329.5059 Evaluate side-chains 258 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.206858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.168637 restraints weight = 48149.862| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.17 r_work: 0.3690 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18762 Z= 0.134 Angle : 0.564 5.098 25356 Z= 0.298 Chirality : 0.040 0.128 2916 Planarity : 0.005 0.055 3012 Dihedral : 8.448 59.811 3624 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.92 % Allowed : 12.32 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.17), residues: 2100 helix: 2.30 (0.13), residues: 1440 sheet: 1.05 (0.40), residues: 144 loop : -1.23 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 24 TYR 0.013 0.002 TYR H 67 PHE 0.012 0.002 PHE G 93 TRP 0.004 0.001 TRP D 79 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00280 (18732) covalent geometry : angle 0.56167 (25296) SS BOND : bond 0.00444 ( 30) SS BOND : angle 1.17643 ( 60) hydrogen bonds : bond 0.06136 ( 1152) hydrogen bonds : angle 3.96154 ( 3420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12861.13 seconds wall clock time: 218 minutes 0.93 seconds (13080.93 seconds total)