Starting phenix.real_space_refine on Tue Aug 26 06:49:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkp_34856/08_2025/8hkp_34856.map" } resolution = 3.6 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= 0.005 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 11364 2.51 5 N 2712 2.21 5 O 3024 1.98 5 H 16842 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s 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: 34098 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "B" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "C" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "E" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "H" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "I" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "K" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "L" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.16 Number of scatterers: 34098 At special positions: 0 Unit cell: (116.048, 104.579, 148.434, 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 3024 8.00 N 2712 7.00 C 11364 6.00 H 16842 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 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: 2.68 Conformation dependent library (CDL) restraints added in 814.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 71.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.758A pdb=" N ILE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.825A pdb=" N ALA A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.521A pdb=" N TYR A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.374A pdb=" N PHE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 221 Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.982A pdb=" N VAL A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.597A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 removed outlier: 4.044A pdb=" N ALA B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 66 " --> pdb=" O CYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 92 removed outlier: 3.624A pdb=" N TYR B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.822A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 Processing helix chain 'B' and resid 248 through 274 removed outlier: 4.072A pdb=" N VAL B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.599A pdb=" N VAL C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.981A pdb=" N ASP C 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP C 48 " --> pdb=" O VAL C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 48' Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.827A pdb=" N ALA C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 92 removed outlier: 3.523A pdb=" N TYR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 92 through 100 removed outlier: 4.102A pdb=" N VAL C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 221 Processing helix chain 'C' and resid 248 through 273 removed outlier: 4.033A pdb=" N VAL C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.621A pdb=" N VAL D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.851A pdb=" N ALA D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 101 removed outlier: 3.628A pdb=" N TYR D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 4.386A pdb=" N PHE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 221 Processing helix chain 'D' and resid 248 through 274 removed outlier: 4.046A pdb=" N VAL D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.591A pdb=" N VAL E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.945A pdb=" N ALA E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 101 removed outlier: 3.540A pdb=" N TYR E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 4.363A pdb=" N PHE E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 221 Processing helix chain 'E' and resid 248 through 274 removed outlier: 4.049A pdb=" N VAL E 252 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 34 through 41 removed outlier: 3.590A pdb=" N VAL F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 48 removed outlier: 4.043A pdb=" N ASP F 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP F 48 " --> pdb=" O VAL F 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 44 through 48' Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.834A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 92 removed outlier: 3.523A pdb=" N TYR F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.854A pdb=" N TYR F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 221 Processing helix chain 'F' and resid 248 through 274 removed outlier: 4.033A pdb=" N VAL F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 41 removed outlier: 3.969A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 48 removed outlier: 4.443A pdb=" N ASP G 48 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.793A pdb=" N ALA G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.591A pdb=" N TYR G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR G 88 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Proline residue: G 89 - end of helix Processing helix chain 'G' and resid 195 through 221 removed outlier: 3.574A pdb=" N TYR G 221 " --> pdb=" O GLN G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.897A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 41 removed outlier: 4.043A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 48 removed outlier: 4.366A pdb=" N ASP H 48 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 4.007A pdb=" N ALA H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 99 removed outlier: 3.553A pdb=" N TYR H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS H 87 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 195 through 221 removed outlier: 3.553A pdb=" N TYR H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.918A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 46 removed outlier: 3.822A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 71 removed outlier: 3.717A pdb=" N ALA I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 99 removed outlier: 3.616A pdb=" N TYR I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS I 87 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR I 88 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Proline residue: I 89 - end of helix Processing helix chain 'I' and resid 195 through 221 removed outlier: 3.553A pdb=" N TYR I 221 " --> pdb=" O GLN I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.893A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 41 removed outlier: 4.009A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 48 removed outlier: 4.470A pdb=" N ASP J 48 " --> pdb=" O VAL J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 71 removed outlier: 3.889A pdb=" N ALA J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 99 removed outlier: 3.609A pdb=" N TYR J 78 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS J 87 " --> pdb=" O ILE J 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Proline residue: J 89 - end of helix Processing helix chain 'J' and resid 195 through 221 removed outlier: 3.565A pdb=" N TYR J 221 " --> pdb=" O GLN J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 276 removed outlier: 3.735A pdb=" N VAL J 252 " --> pdb=" O THR J 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 41 removed outlier: 4.175A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 48 removed outlier: 4.381A pdb=" N ASP K 48 " --> pdb=" O VAL K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.791A pdb=" N ALA K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 99 removed outlier: 3.506A pdb=" N TYR K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS K 87 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR K 88 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Proline residue: K 89 - end of helix Processing helix chain 'K' and resid 195 through 221 removed outlier: 3.567A pdb=" N TYR K 221 " --> pdb=" O GLN K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.939A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 41 removed outlier: 3.966A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.831A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.688A 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 removed outlier: 3.716A pdb=" N ALA L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 86 removed outlier: 3.633A pdb=" N TYR L 78 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 99 Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.555A pdb=" N TYR L 221 " --> pdb=" O GLN L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.844A 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: 3.788A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.799A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.771A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.789A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.799A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.782A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 228 through 231 Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.779A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 228 through 231 Processing sheet with id=AB1, first strand: chain 'J' and resid 228 through 231 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.741A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 228 through 231 1064 hydrogen bonds defined for protein. 3144 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: 6.05 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16806 1.03 - 1.23: 100 1.23 - 1.43: 7388 1.43 - 1.62: 10014 1.62 - 1.82: 222 Bond restraints: 34530 Sorted by residual: bond pdb=" CBK AV0 D 401 " pdb=" CBQ AV0 D 401 " ideal model delta sigma weight residual 1.525 1.655 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" CBK AV0 F 401 " pdb=" CBQ AV0 F 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CBK AV0 B 401 " pdb=" CBQ AV0 B 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CBK AV0 E 401 " pdb=" CBQ AV0 E 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" CBK AV0 A 401 " pdb=" CBQ AV0 A 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 34525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 60043 1.39 - 2.78: 1686 2.78 - 4.17: 238 4.17 - 5.57: 58 5.57 - 6.96: 15 Bond angle restraints: 62040 Sorted by residual: angle pdb=" N ILE F 237 " pdb=" CA ILE F 237 " pdb=" C ILE F 237 " ideal model delta sigma weight residual 106.55 111.71 -5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N ILE G 195 " pdb=" CA ILE G 195 " pdb=" C ILE G 195 " ideal model delta sigma weight residual 111.62 108.87 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" N ILE J 195 " pdb=" CA ILE J 195 " pdb=" C ILE J 195 " ideal model delta sigma weight residual 111.62 108.88 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" N ILE L 195 " pdb=" CA ILE L 195 " pdb=" C ILE L 195 " ideal model delta sigma weight residual 111.62 108.90 2.72 7.90e-01 1.60e+00 1.18e+01 angle pdb=" N ILE H 195 " pdb=" CA ILE H 195 " pdb=" C ILE H 195 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 ... (remaining 62035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 16271 35.96 - 71.92: 497 71.92 - 107.88: 81 107.88 - 143.85: 83 143.85 - 179.81: 12 Dihedral angle restraints: 16944 sinusoidal: 9294 harmonic: 7650 Sorted by residual: dihedral pdb=" CCH AV0 C 401 " pdb=" CCQ AV0 C 401 " pdb=" OCB AV0 C 401 " pdb=" CCS AV0 C 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.80 -179.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CCH AV0 F 401 " pdb=" CCQ AV0 F 401 " pdb=" OCB AV0 F 401 " pdb=" CCS AV0 F 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.85 -179.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CCH AV0 B 401 " pdb=" CCQ AV0 B 401 " pdb=" OCB AV0 B 401 " pdb=" CCS AV0 B 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.25 179.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 16941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1850 0.039 - 0.077: 763 0.077 - 0.116: 197 0.116 - 0.154: 28 0.154 - 0.193: 12 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CCV AV0 B 401 " pdb=" CCR AV0 B 401 " pdb=" CCT AV0 B 401 " pdb=" OAU AV0 B 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CCV AV0 E 401 " pdb=" CCR AV0 E 401 " pdb=" CCT AV0 E 401 " pdb=" OAU AV0 E 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CCV AV0 F 401 " pdb=" CCR AV0 F 401 " pdb=" CCT AV0 F 401 " pdb=" OAU AV0 F 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2847 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 246 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO H 247 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO H 247 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 247 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 246 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO K 247 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO K 247 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 247 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 246 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO L 247 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.031 5.00e-02 4.00e+02 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2837 2.23 - 2.82: 72410 2.82 - 3.42: 78649 3.42 - 4.01: 107476 4.01 - 4.60: 169698 Nonbonded interactions: 431070 Sorted by model distance: nonbonded pdb="HH11 ARG A 77 " pdb=" OE2 GLU B 249 " model vdw 1.639 2.450 nonbonded pdb="HH11 ARG B 77 " pdb=" OE2 GLU C 249 " model vdw 1.686 2.450 nonbonded pdb=" O ILE L 73 " pdb=" HH TYR L 221 " model vdw 1.692 2.450 nonbonded pdb=" O ILE G 73 " pdb=" HH TYR G 221 " model vdw 1.692 2.450 nonbonded pdb="HH11 ARG E 77 " pdb=" OE2 GLU F 249 " model vdw 1.698 2.450 ... (remaining 431065 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 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'B' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'E' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'F' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'G' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'H' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'I' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'J' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'K' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'L' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) } 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 group one per residue 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: 4.570 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: 0.130 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.410 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.009 0.130 17724 Z= 0.439 Angle : 0.683 6.958 24132 Z= 0.353 Chirality : 0.044 0.193 2850 Planarity : 0.004 0.056 2904 Dihedral : 23.505 179.808 6828 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.19 (0.16), residues: 2040 helix: -0.53 (0.13), residues: 1326 sheet: -2.17 (0.43), residues: 120 loop : -3.25 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.009 0.001 TYR J 218 PHE 0.021 0.001 PHE J 33 TRP 0.006 0.001 TRP L 79 HIS 0.006 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00933 (17688) covalent geometry : angle 0.68283 (24060) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.74376 ( 72) hydrogen bonds : bond 0.10822 ( 1064) hydrogen bonds : angle 4.95937 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.853 Fit side-chains REVERT: B 100 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7750 (mm-40) REVERT: C 100 GLN cc_start: 0.7638 (tp40) cc_final: 0.7160 (tm-30) REVERT: K 69 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7413 (tpp80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2961 time to fit residues: 106.4466 Evaluate side-chains 207 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108636 restraints weight = 60354.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.111896 restraints weight = 28147.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113873 restraints weight = 18293.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114962 restraints weight = 14385.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.115598 restraints weight = 12627.624| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17724 Z= 0.170 Angle : 0.669 9.897 24132 Z= 0.322 Chirality : 0.043 0.185 2850 Planarity : 0.004 0.053 2904 Dihedral : 22.786 174.787 3048 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.74 % Allowed : 5.15 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.19), residues: 2040 helix: 1.30 (0.14), residues: 1338 sheet: -1.56 (0.45), residues: 120 loop : -2.68 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 278 TYR 0.010 0.001 TYR G 218 PHE 0.017 0.001 PHE J 33 TRP 0.006 0.001 TRP J 79 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (17688) covalent geometry : angle 0.66729 (24060) SS BOND : bond 0.00161 ( 36) SS BOND : angle 1.02723 ( 72) hydrogen bonds : bond 0.05989 ( 1064) hydrogen bonds : angle 3.99802 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.612 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 216 average time/residue: 0.2592 time to fit residues: 85.1196 Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 207 ASN B 207 ASN C 59 GLN D 59 GLN D 207 ASN E 59 GLN E 207 ASN F 59 GLN G 59 GLN H 59 GLN H 75 HIS I 59 GLN I 100 GLN J 59 GLN K 59 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.096834 restraints weight = 61598.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.100289 restraints weight = 28073.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.102344 restraints weight = 17756.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.103483 restraints weight = 13746.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.104189 restraints weight = 11949.174| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17724 Z= 0.152 Angle : 0.648 10.241 24132 Z= 0.304 Chirality : 0.043 0.303 2850 Planarity : 0.004 0.049 2904 Dihedral : 17.841 165.999 3048 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.37 % Allowed : 6.74 % Favored : 92.89 % 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: 1.02 (0.19), residues: 2040 helix: 2.06 (0.14), residues: 1338 sheet: -1.03 (0.47), residues: 120 loop : -2.41 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 278 TYR 0.012 0.001 TYR C 96 PHE 0.018 0.001 PHE J 33 TRP 0.004 0.001 TRP L 277 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (17688) covalent geometry : angle 0.64715 (24060) SS BOND : bond 0.00210 ( 36) SS BOND : angle 0.95894 ( 72) hydrogen bonds : bond 0.05595 ( 1064) hydrogen bonds : angle 3.73016 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 PHE cc_start: 0.8295 (t80) cc_final: 0.8020 (t80) REVERT: G 238 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7526 (pttp) REVERT: I 52 MET cc_start: 0.9031 (mmt) cc_final: 0.8700 (mmt) REVERT: I 278 ARG cc_start: 0.6754 (mtp85) cc_final: 0.5854 (ptt-90) REVERT: K 52 MET cc_start: 0.9029 (mmm) cc_final: 0.8829 (mmt) REVERT: L 52 MET cc_start: 0.9031 (mmt) cc_final: 0.8716 (mmt) outliers start: 7 outliers final: 3 residues processed: 245 average time/residue: 0.2706 time to fit residues: 100.2206 Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 268 ASN C 59 GLN C 232 ASN D 59 GLN D 268 ASN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN K 75 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.092095 restraints weight = 62183.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.095554 restraints weight = 29022.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.097577 restraints weight = 18517.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.098822 restraints weight = 14418.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.099377 restraints weight = 12482.267| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17724 Z= 0.145 Angle : 0.588 6.760 24132 Z= 0.287 Chirality : 0.043 0.285 2850 Planarity : 0.004 0.049 2904 Dihedral : 16.877 169.103 3048 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.42 % Allowed : 8.33 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.19), residues: 2040 helix: 2.42 (0.14), residues: 1338 sheet: -0.66 (0.49), residues: 120 loop : -2.19 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 197 TYR 0.010 0.001 TYR G 218 PHE 0.017 0.001 PHE J 33 TRP 0.004 0.001 TRP H 277 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (17688) covalent geometry : angle 0.58690 (24060) SS BOND : bond 0.00184 ( 36) SS BOND : angle 0.95799 ( 72) hydrogen bonds : bond 0.05389 ( 1064) hydrogen bonds : angle 3.60625 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 238 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7597 (pttp) REVERT: I 52 MET cc_start: 0.9062 (mmt) cc_final: 0.8788 (mmt) REVERT: L 52 MET cc_start: 0.9060 (mmt) cc_final: 0.8742 (mmt) outliers start: 8 outliers final: 3 residues processed: 244 average time/residue: 0.2490 time to fit residues: 94.4618 Evaluate side-chains 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain J residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.110679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.088062 restraints weight = 63288.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.090867 restraints weight = 33736.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.092578 restraints weight = 23170.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.093580 restraints weight = 18660.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.094203 restraints weight = 16444.806| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17724 Z= 0.217 Angle : 0.620 5.545 24132 Z= 0.314 Chirality : 0.044 0.294 2850 Planarity : 0.004 0.053 2904 Dihedral : 16.405 171.979 3048 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.64 % Allowed : 9.02 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.19), residues: 2040 helix: 2.39 (0.14), residues: 1338 sheet: -0.46 (0.49), residues: 120 loop : -2.14 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 278 TYR 0.018 0.002 TYR A 218 PHE 0.014 0.001 PHE J 33 TRP 0.005 0.001 TRP A 79 HIS 0.006 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00529 (17688) covalent geometry : angle 0.61784 (24060) SS BOND : bond 0.00175 ( 36) SS BOND : angle 1.14815 ( 72) hydrogen bonds : bond 0.06229 ( 1064) hydrogen bonds : angle 3.72662 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 ASP cc_start: 0.8750 (t70) cc_final: 0.8501 (t0) REVERT: I 52 MET cc_start: 0.9092 (mmt) cc_final: 0.8839 (mmt) REVERT: L 52 MET cc_start: 0.9099 (mmt) cc_final: 0.8787 (mmt) outliers start: 12 outliers final: 6 residues processed: 247 average time/residue: 0.2579 time to fit residues: 97.1999 Evaluate side-chains 241 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.115052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.092555 restraints weight = 61732.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.095413 restraints weight = 32711.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.097196 restraints weight = 22398.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.098252 restraints weight = 17967.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.098664 restraints weight = 15802.517| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17724 Z= 0.104 Angle : 0.502 5.015 24132 Z= 0.257 Chirality : 0.040 0.205 2850 Planarity : 0.004 0.048 2904 Dihedral : 16.008 174.970 3048 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.48 % Allowed : 9.24 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.13 (0.19), residues: 2040 helix: 2.94 (0.14), residues: 1338 sheet: -0.48 (0.50), residues: 120 loop : -2.07 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 278 TYR 0.008 0.001 TYR J 218 PHE 0.011 0.001 PHE L 205 TRP 0.003 0.000 TRP L 277 HIS 0.004 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00224 (17688) covalent geometry : angle 0.50084 (24060) SS BOND : bond 0.00210 ( 36) SS BOND : angle 0.76027 ( 72) hydrogen bonds : bond 0.04705 ( 1064) hydrogen bonds : angle 3.41960 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8725 (mmt) cc_final: 0.8441 (mmp) REVERT: H 253 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: I 52 MET cc_start: 0.9067 (mmt) cc_final: 0.8780 (mmt) REVERT: I 253 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: I 278 ARG cc_start: 0.6901 (mtp85) cc_final: 0.5986 (ptt-90) REVERT: L 52 MET cc_start: 0.9073 (mmt) cc_final: 0.8733 (mmt) REVERT: L 253 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7884 (m-80) outliers start: 9 outliers final: 5 residues processed: 240 average time/residue: 0.2509 time to fit residues: 93.8984 Evaluate side-chains 237 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 167 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN K 268 ASN L 59 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.091351 restraints weight = 62461.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.094177 restraints weight = 33277.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.095907 restraints weight = 22840.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.097014 restraints weight = 18314.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.097542 restraints weight = 16185.184| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17724 Z= 0.119 Angle : 0.503 5.083 24132 Z= 0.256 Chirality : 0.039 0.169 2850 Planarity : 0.004 0.045 2904 Dihedral : 15.623 175.586 3048 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.42 % Allowed : 9.71 % Favored : 89.86 % 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: 2.26 (0.19), residues: 2040 helix: 3.02 (0.14), residues: 1338 sheet: -0.42 (0.49), residues: 120 loop : -1.98 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 278 TYR 0.017 0.001 TYR A 218 PHE 0.009 0.001 PHE I 33 TRP 0.003 0.001 TRP L 277 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00278 (17688) covalent geometry : angle 0.50208 (24060) SS BOND : bond 0.00157 ( 36) SS BOND : angle 0.83389 ( 72) hydrogen bonds : bond 0.04815 ( 1064) hydrogen bonds : angle 3.41875 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 233 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8729 (mmt) cc_final: 0.8492 (mmp) REVERT: G 68 ASP cc_start: 0.8706 (t70) cc_final: 0.8428 (t0) REVERT: H 253 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: I 52 MET cc_start: 0.9076 (mmt) cc_final: 0.8763 (mmt) REVERT: I 253 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: I 278 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6043 (ptt-90) REVERT: L 52 MET cc_start: 0.9086 (mmt) cc_final: 0.8752 (mmt) REVERT: L 253 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7818 (m-80) outliers start: 8 outliers final: 4 residues processed: 237 average time/residue: 0.2510 time to fit residues: 93.5151 Evaluate side-chains 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 121 optimal weight: 0.0770 chunk 200 optimal weight: 0.9980 chunk 167 optimal weight: 0.0270 chunk 180 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.116774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.094272 restraints weight = 61524.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.097177 restraints weight = 32437.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098930 restraints weight = 22110.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.100040 restraints weight = 17649.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.100606 restraints weight = 15628.003| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17724 Z= 0.094 Angle : 0.464 5.000 24132 Z= 0.239 Chirality : 0.038 0.122 2850 Planarity : 0.003 0.038 2904 Dihedral : 15.352 179.153 3048 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.58 % Allowed : 9.55 % Favored : 89.86 % 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: 2.59 (0.19), residues: 2040 helix: 3.34 (0.14), residues: 1332 sheet: -0.74 (0.49), residues: 126 loop : -1.87 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 278 TYR 0.017 0.001 TYR A 218 PHE 0.020 0.001 PHE G 205 TRP 0.003 0.000 TRP L 277 HIS 0.004 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00198 (17688) covalent geometry : angle 0.46295 (24060) SS BOND : bond 0.00166 ( 36) SS BOND : angle 0.67906 ( 72) hydrogen bonds : bond 0.03976 ( 1064) hydrogen bonds : angle 3.23150 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8714 (mmt) cc_final: 0.8384 (mmp) REVERT: D 85 MET cc_start: 0.8731 (mmt) cc_final: 0.8453 (mmp) REVERT: H 253 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: I 52 MET cc_start: 0.9049 (mmt) cc_final: 0.8743 (mmt) REVERT: I 253 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: I 278 ARG cc_start: 0.7013 (mtp85) cc_final: 0.5780 (ptm160) REVERT: L 52 MET cc_start: 0.9061 (mmt) cc_final: 0.8698 (mmt) REVERT: L 253 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7784 (m-80) outliers start: 11 outliers final: 6 residues processed: 245 average time/residue: 0.2776 time to fit residues: 108.2908 Evaluate side-chains 239 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 273 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.112805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.090045 restraints weight = 62929.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.092837 restraints weight = 33908.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.094592 restraints weight = 23412.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.095579 restraints weight = 18892.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.095986 restraints weight = 16691.664| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17724 Z= 0.153 Angle : 0.529 5.122 24132 Z= 0.271 Chirality : 0.040 0.154 2850 Planarity : 0.004 0.044 2904 Dihedral : 15.527 179.105 3048 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.48 % Allowed : 9.98 % Favored : 89.54 % 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: 2.42 (0.19), residues: 2040 helix: 3.15 (0.14), residues: 1326 sheet: -0.25 (0.50), residues: 120 loop : -1.83 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 278 TYR 0.019 0.001 TYR A 218 PHE 0.011 0.001 PHE I 33 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (17688) covalent geometry : angle 0.52729 (24060) SS BOND : bond 0.00160 ( 36) SS BOND : angle 0.96935 ( 72) hydrogen bonds : bond 0.04958 ( 1064) hydrogen bonds : angle 3.38781 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8742 (mmt) cc_final: 0.8514 (mmp) REVERT: G 68 ASP cc_start: 0.8741 (t70) cc_final: 0.8463 (t0) REVERT: H 253 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: I 52 MET cc_start: 0.9095 (mmt) cc_final: 0.8795 (mmt) REVERT: I 253 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: I 278 ARG cc_start: 0.7083 (mtp85) cc_final: 0.5817 (ptm160) REVERT: L 52 MET cc_start: 0.9106 (mmt) cc_final: 0.8743 (mmt) REVERT: L 253 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7869 (m-80) outliers start: 9 outliers final: 5 residues processed: 228 average time/residue: 0.2589 time to fit residues: 93.3718 Evaluate side-chains 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN D 59 GLN E 59 GLN H 59 GLN I 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.090357 restraints weight = 63095.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.093187 restraints weight = 33847.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.094918 restraints weight = 23334.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.095919 restraints weight = 18826.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.096553 restraints weight = 16582.938| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17724 Z= 0.129 Angle : 0.502 5.096 24132 Z= 0.260 Chirality : 0.039 0.125 2850 Planarity : 0.004 0.043 2904 Dihedral : 15.580 179.602 3048 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.48 % Allowed : 10.03 % Favored : 89.49 % 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: 2.55 (0.19), residues: 2040 helix: 3.24 (0.14), residues: 1332 sheet: -0.26 (0.50), residues: 120 loop : -1.78 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 278 TYR 0.017 0.001 TYR A 218 PHE 0.012 0.001 PHE I 33 TRP 0.003 0.001 TRP G 79 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00305 (17688) covalent geometry : angle 0.50036 (24060) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.85634 ( 72) hydrogen bonds : bond 0.04806 ( 1064) hydrogen bonds : angle 3.35959 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8735 (mmt) cc_final: 0.8469 (mmp) REVERT: G 68 ASP cc_start: 0.8735 (t70) cc_final: 0.8467 (t0) REVERT: H 253 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: I 52 MET cc_start: 0.9096 (mmt) cc_final: 0.8802 (mmt) REVERT: I 253 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: I 278 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6094 (ptt-90) REVERT: L 52 MET cc_start: 0.9090 (mmt) cc_final: 0.8737 (mmt) REVERT: L 253 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7893 (m-80) outliers start: 9 outliers final: 6 residues processed: 226 average time/residue: 0.2450 time to fit residues: 87.9487 Evaluate side-chains 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.0010 chunk 121 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.093315 restraints weight = 62348.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.096168 restraints weight = 33308.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.097938 restraints weight = 22904.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.098947 restraints weight = 18457.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.099487 restraints weight = 16320.002| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17724 Z= 0.092 Angle : 0.461 5.005 24132 Z= 0.240 Chirality : 0.038 0.121 2850 Planarity : 0.003 0.040 2904 Dihedral : 15.369 179.986 3048 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.53 % Allowed : 10.35 % Favored : 89.12 % 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: 2.73 (0.19), residues: 2040 helix: 3.44 (0.14), residues: 1320 sheet: -0.54 (0.49), residues: 126 loop : -1.70 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 278 TYR 0.018 0.001 TYR A 218 PHE 0.021 0.001 PHE J 205 TRP 0.003 0.000 TRP L 277 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00198 (17688) covalent geometry : angle 0.45997 (24060) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.67414 ( 72) hydrogen bonds : bond 0.04024 ( 1064) hydrogen bonds : angle 3.21770 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.47 seconds wall clock time: 73 minutes 44.99 seconds (4424.99 seconds total)