Starting phenix.real_space_refine on Sun Jun 29 11:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkp_34856/06_2025/8hkp_34856_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkp_34856/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkp_34856/06_2025/8hkp_34856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkp_34856/06_2025/8hkp_34856.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkp_34856/06_2025/8hkp_34856_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkp_34856/06_2025/8hkp_34856_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.81, per 1000 atoms: 0.58 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: 8.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.39 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: 13.39 Time building geometry restraints manager: 10.57 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: 0.02 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: 0.010 Normalize map: mean=0, sd=1: 2.730 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: 0.540 Extract box with map and model: 1.430 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 74.540 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (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 TRP 0.006 0.001 TRP L 79 HIS 0.006 0.001 HIS J 75 PHE 0.021 0.001 PHE J 33 TYR 0.009 0.001 TYR J 218 ARG 0.003 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.10822 ( 1064) hydrogen bonds : angle 4.95937 ( 3144) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.74376 ( 72) covalent geometry : bond 0.00933 (17688) covalent geometry : angle 0.68283 (24060) *********************** 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 : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash 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: I 278 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5141 (ptm160) REVERT: K 69 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7414 (tpp80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.7046 time to fit residues: 252.9630 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 : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN C 59 GLN E 59 GLN F 59 GLN G 59 GLN I 59 GLN J 59 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.103278 restraints weight = 60306.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.106706 restraints weight = 28612.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108766 restraints weight = 18483.713| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1233 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= 0.137 Angle : 0.644 9.473 24132 Z= 0.307 Chirality : 0.042 0.188 2850 Planarity : 0.004 0.050 2904 Dihedral : 22.124 173.312 3048 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.69 % Allowed : 5.15 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 2040 helix: 1.52 (0.14), residues: 1338 sheet: -1.60 (0.45), residues: 120 loop : -2.64 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 79 HIS 0.005 0.001 HIS J 75 PHE 0.017 0.001 PHE J 33 TYR 0.009 0.001 TYR G 218 ARG 0.003 0.000 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 1064) hydrogen bonds : angle 3.88254 ( 3144) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.91164 ( 72) covalent geometry : bond 0.00298 (17688) covalent geometry : angle 0.64338 (24060) *********************** 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 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7400 (ttt-90) REVERT: I 278 ARG cc_start: 0.5859 (mtp85) cc_final: 0.5076 (ptm160) outliers start: 13 outliers final: 13 residues processed: 219 average time/residue: 0.6609 time to fit residues: 224.2873 Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 224 SER 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 129 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 chunk 101 optimal weight: 5.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 59 GLN 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 I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106987 restraints weight = 59824.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110441 restraints weight = 27230.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112470 restraints weight = 17322.771| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17724 Z= 0.125 Angle : 0.648 10.113 24132 Z= 0.293 Chirality : 0.043 0.318 2850 Planarity : 0.004 0.045 2904 Dihedral : 17.229 166.003 3048 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.32 % Allowed : 6.85 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2040 helix: 2.27 (0.14), residues: 1356 sheet: -1.15 (0.47), residues: 120 loop : -2.52 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 277 HIS 0.004 0.001 HIS I 75 PHE 0.018 0.001 PHE J 33 TYR 0.009 0.001 TYR J 218 ARG 0.002 0.000 ARG I 197 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 1064) hydrogen bonds : angle 3.59332 ( 3144) SS BOND : bond 0.00191 ( 36) SS BOND : angle 0.82557 ( 72) covalent geometry : bond 0.00286 (17688) covalent geometry : angle 0.64744 (24060) *********************** 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 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 227 time to evaluate : 6.279 Fit side-chains revert: symmetry clash REVERT: G 238 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7356 (pttp) REVERT: I 52 MET cc_start: 0.8982 (mmt) cc_final: 0.8686 (mmt) REVERT: L 52 MET cc_start: 0.8963 (mmt) cc_final: 0.8640 (mmt) outliers start: 6 outliers final: 3 residues processed: 230 average time/residue: 1.1539 time to fit residues: 433.5191 Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 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 144 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 59 GLN E 59 GLN F 59 GLN G 59 GLN H 75 HIS I 59 GLN J 59 GLN K 75 HIS L 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.090446 restraints weight = 62912.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.093839 restraints weight = 29491.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.095888 restraints weight = 18880.919| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17724 Z= 0.194 Angle : 0.644 6.496 24132 Z= 0.318 Chirality : 0.044 0.289 2850 Planarity : 0.004 0.053 2904 Dihedral : 17.056 171.580 3048 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.48 % Allowed : 8.39 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2040 helix: 2.36 (0.14), residues: 1338 sheet: -0.66 (0.48), residues: 120 loop : -2.20 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.006 0.001 HIS H 75 PHE 0.016 0.001 PHE J 33 TYR 0.018 0.002 TYR D 218 ARG 0.006 0.000 ARG I 278 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 1064) hydrogen bonds : angle 3.69552 ( 3144) SS BOND : bond 0.00186 ( 36) SS BOND : angle 1.14173 ( 72) covalent geometry : bond 0.00467 (17688) covalent geometry : angle 0.64214 (24060) *********************** 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 253 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 5.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 238 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7659 (pttp) REVERT: I 52 MET cc_start: 0.9071 (mmt) cc_final: 0.8804 (mmt) REVERT: I 278 ARG cc_start: 0.6810 (mtp85) cc_final: 0.5466 (tpt90) REVERT: K 33 PHE cc_start: 0.8419 (t80) cc_final: 0.8173 (t80) REVERT: L 52 MET cc_start: 0.9073 (mmt) cc_final: 0.8769 (mmt) outliers start: 9 outliers final: 4 residues processed: 249 average time/residue: 0.9861 time to fit residues: 381.0465 Evaluate side-chains 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 228 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 153 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN D 59 GLN H 59 GLN K 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.096906 restraints weight = 61842.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.100264 restraints weight = 28435.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.102291 restraints weight = 18009.312| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2654 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= 0.125 Angle : 0.541 5.057 24132 Z= 0.272 Chirality : 0.041 0.263 2850 Planarity : 0.004 0.046 2904 Dihedral : 16.224 171.401 3048 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.74 % Allowed : 8.76 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 2040 helix: 2.70 (0.14), residues: 1338 sheet: -0.51 (0.49), residues: 120 loop : -2.14 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 277 HIS 0.005 0.001 HIS J 75 PHE 0.014 0.001 PHE J 33 TYR 0.009 0.001 TYR J 218 ARG 0.002 0.000 ARG J 197 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 1064) hydrogen bonds : angle 3.54324 ( 3144) SS BOND : bond 0.00183 ( 36) SS BOND : angle 0.89679 ( 72) covalent geometry : bond 0.00287 (17688) covalent geometry : angle 0.53921 (24060) *********************** 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 248 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 238 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7637 (pttp) REVERT: H 253 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: I 52 MET cc_start: 0.9085 (mmt) cc_final: 0.8811 (mmt) REVERT: I 253 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: I 278 ARG cc_start: 0.6819 (mtp85) cc_final: 0.5592 (tpt90) REVERT: J 52 MET cc_start: 0.9083 (mmm) cc_final: 0.8880 (mmt) REVERT: K 33 PHE cc_start: 0.8385 (t80) cc_final: 0.8145 (t80) REVERT: L 52 MET cc_start: 0.9075 (mmt) cc_final: 0.8703 (mmt) outliers start: 14 outliers final: 6 residues processed: 242 average time/residue: 0.5676 time to fit residues: 213.4663 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 : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain G residue 238 LYS 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 L residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.113179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.089993 restraints weight = 62767.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.093110 restraints weight = 31302.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.095020 restraints weight = 20756.362| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17724 Z= 0.146 Angle : 0.539 5.118 24132 Z= 0.273 Chirality : 0.040 0.188 2850 Planarity : 0.004 0.048 2904 Dihedral : 15.764 175.049 3048 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.58 % Allowed : 9.24 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 2040 helix: 2.85 (0.14), residues: 1338 sheet: -0.43 (0.49), residues: 120 loop : -2.01 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 277 HIS 0.005 0.001 HIS G 75 PHE 0.014 0.001 PHE K 33 TYR 0.010 0.001 TYR G 218 ARG 0.003 0.000 ARG I 278 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 1064) hydrogen bonds : angle 3.50085 ( 3144) SS BOND : bond 0.00175 ( 36) SS BOND : angle 0.94681 ( 72) covalent geometry : bond 0.00349 (17688) covalent geometry : angle 0.53745 (24060) *********************** 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 248 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 24 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.7249 (mtm-85) REVERT: F 97 SER cc_start: 0.9116 (t) cc_final: 0.8898 (p) REVERT: G 68 ASP cc_start: 0.8668 (t70) cc_final: 0.8395 (t0) REVERT: G 238 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7640 (pttp) REVERT: H 253 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: I 52 MET cc_start: 0.9099 (mmt) cc_final: 0.8813 (mmt) REVERT: I 253 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: I 278 ARG cc_start: 0.6988 (mtp85) cc_final: 0.5672 (tpt90) REVERT: J 52 MET cc_start: 0.9122 (mmm) cc_final: 0.8919 (mmt) REVERT: K 33 PHE cc_start: 0.8414 (t80) cc_final: 0.8179 (t80) REVERT: L 52 MET cc_start: 0.9116 (mmt) cc_final: 0.8777 (mmt) outliers start: 11 outliers final: 7 residues processed: 241 average time/residue: 0.5971 time to fit residues: 224.6914 Evaluate side-chains 244 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 238 LYS 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 269 LEU Chi-restraints excluded: chain L residue 273 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 59 GLN F 59 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN I 59 GLN J 59 GLN K 59 GLN L 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.111203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.087723 restraints weight = 63577.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.090873 restraints weight = 31305.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.092762 restraints weight = 20554.000| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17724 Z= 0.168 Angle : 0.558 5.162 24132 Z= 0.286 Chirality : 0.041 0.161 2850 Planarity : 0.004 0.048 2904 Dihedral : 15.853 179.895 3048 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.64 % Allowed : 9.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 2040 helix: 2.84 (0.14), residues: 1338 sheet: -0.32 (0.49), residues: 120 loop : -2.00 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 79 HIS 0.006 0.001 HIS G 75 PHE 0.019 0.001 PHE J 205 TYR 0.024 0.001 TYR A 218 ARG 0.002 0.000 ARG K 197 Details of bonding type rmsd hydrogen bonds : bond 0.05680 ( 1064) hydrogen bonds : angle 3.57269 ( 3144) SS BOND : bond 0.00167 ( 36) SS BOND : angle 1.03401 ( 72) covalent geometry : bond 0.00406 (17688) covalent geometry : angle 0.55562 (24060) *********************** 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 252 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 ASP cc_start: 0.8720 (t70) cc_final: 0.8485 (t0) REVERT: H 253 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: I 52 MET cc_start: 0.9119 (mmt) cc_final: 0.8848 (mmt) REVERT: I 253 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: I 278 ARG cc_start: 0.7101 (mtp85) cc_final: 0.5772 (tpt90) REVERT: J 68 ASP cc_start: 0.8656 (t70) cc_final: 0.8440 (t0) REVERT: K 33 PHE cc_start: 0.8431 (t80) cc_final: 0.8147 (t80) REVERT: L 52 MET cc_start: 0.9137 (mmt) cc_final: 0.8817 (mmt) REVERT: L 253 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7817 (m-80) outliers start: 12 outliers final: 7 residues processed: 245 average time/residue: 0.6260 time to fit residues: 233.3863 Evaluate side-chains 247 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 2.513 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 273 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 59 GLN D 59 GLN G 59 GLN H 59 GLN K 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.085991 restraints weight = 64153.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.089018 restraints weight = 32717.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.090868 restraints weight = 21791.636| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17724 Z= 0.211 Angle : 0.592 5.375 24132 Z= 0.304 Chirality : 0.042 0.167 2850 Planarity : 0.004 0.051 2904 Dihedral : 15.867 179.581 3048 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.64 % Allowed : 10.35 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2040 helix: 2.76 (0.14), residues: 1338 sheet: -0.30 (0.49), residues: 120 loop : -1.97 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 79 HIS 0.007 0.001 HIS J 75 PHE 0.011 0.001 PHE I 33 TYR 0.019 0.002 TYR D 218 ARG 0.003 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.06167 ( 1064) hydrogen bonds : angle 3.65596 ( 3144) SS BOND : bond 0.00191 ( 36) SS BOND : angle 1.16067 ( 72) covalent geometry : bond 0.00517 (17688) covalent geometry : angle 0.58940 (24060) *********************** 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 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 253 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: I 52 MET cc_start: 0.9128 (mmt) cc_final: 0.8865 (mmt) REVERT: I 253 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: I 278 ARG cc_start: 0.7176 (mtp85) cc_final: 0.5742 (tpt90) REVERT: L 52 MET cc_start: 0.9145 (mmt) cc_final: 0.8844 (mmt) REVERT: L 253 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7844 (m-80) outliers start: 12 outliers final: 8 residues processed: 252 average time/residue: 0.6784 time to fit residues: 261.6900 Evaluate side-chains 252 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU 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 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 28 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.113719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.090259 restraints weight = 62774.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.093468 restraints weight = 30727.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.095482 restraints weight = 20078.329| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17724 Z= 0.101 Angle : 0.491 5.059 24132 Z= 0.254 Chirality : 0.039 0.123 2850 Planarity : 0.004 0.046 2904 Dihedral : 15.512 178.768 3048 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.58 % Allowed : 10.62 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2040 helix: 3.15 (0.14), residues: 1332 sheet: -0.63 (0.48), residues: 126 loop : -1.86 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 277 HIS 0.012 0.001 HIS K 274 PHE 0.011 0.001 PHE I 205 TYR 0.017 0.001 TYR A 218 ARG 0.002 0.000 ARG H 246 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1064) hydrogen bonds : angle 3.37774 ( 3144) SS BOND : bond 0.00201 ( 36) SS BOND : angle 0.75761 ( 72) covalent geometry : bond 0.00219 (17688) covalent geometry : angle 0.48995 (24060) *********************** 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 245 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 234 time to evaluate : 2.592 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8758 (mmt) cc_final: 0.8452 (mmp) REVERT: G 68 ASP cc_start: 0.8684 (t70) cc_final: 0.8423 (t0) REVERT: H 253 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: I 52 MET cc_start: 0.9104 (mmt) cc_final: 0.8806 (mmt) REVERT: I 253 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: I 278 ARG cc_start: 0.7095 (mtp85) cc_final: 0.5783 (tpt90) REVERT: L 52 MET cc_start: 0.9125 (mmt) cc_final: 0.8779 (mmt) REVERT: L 253 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7811 (m-80) outliers start: 11 outliers final: 8 residues processed: 237 average time/residue: 0.5845 time to fit residues: 216.1552 Evaluate side-chains 240 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU 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 Chi-restraints excluded: chain L residue 273 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 172 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.114019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.090788 restraints weight = 62746.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.093902 restraints weight = 31423.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.095773 restraints weight = 20843.340| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3496 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= 0.103 Angle : 0.487 6.433 24132 Z= 0.251 Chirality : 0.038 0.123 2850 Planarity : 0.003 0.044 2904 Dihedral : 15.358 179.527 3048 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.37 % Allowed : 11.20 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 2040 helix: 3.28 (0.14), residues: 1332 sheet: -0.58 (0.49), residues: 126 loop : -1.71 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 277 HIS 0.011 0.001 HIS K 274 PHE 0.008 0.001 PHE L 205 TYR 0.017 0.001 TYR D 218 ARG 0.002 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1064) hydrogen bonds : angle 3.33722 ( 3144) SS BOND : bond 0.00359 ( 36) SS BOND : angle 0.80125 ( 72) covalent geometry : bond 0.00233 (17688) covalent geometry : angle 0.48556 (24060) ********************** 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 237 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8767 (mmt) cc_final: 0.8460 (mmp) REVERT: G 68 ASP cc_start: 0.8696 (t70) cc_final: 0.8401 (t0) REVERT: H 253 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: I 52 MET cc_start: 0.9099 (mmt) cc_final: 0.8808 (mmt) REVERT: I 253 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: I 278 ARG cc_start: 0.7107 (mtp85) cc_final: 0.5796 (tpt90) REVERT: L 52 MET cc_start: 0.9130 (mmt) cc_final: 0.8721 (mmt) REVERT: L 253 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7847 (m-80) outliers start: 7 outliers final: 3 residues processed: 233 average time/residue: 0.5789 time to fit residues: 211.2099 Evaluate side-chains 230 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3149 r_free = 0.3149 target = 0.113176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.089885 restraints weight = 63360.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.092973 restraints weight = 31785.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.094894 restraints weight = 21085.709| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3539 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= 0.122 Angle : 0.501 5.494 24132 Z= 0.259 Chirality : 0.039 0.124 2850 Planarity : 0.004 0.046 2904 Dihedral : 15.345 179.373 3048 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.58 % Allowed : 10.62 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 2040 helix: 3.27 (0.14), residues: 1332 sheet: -0.55 (0.49), residues: 126 loop : -1.69 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 277 HIS 0.012 0.001 HIS K 274 PHE 0.009 0.001 PHE I 33 TYR 0.025 0.001 TYR D 218 ARG 0.002 0.000 ARG L 197 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1064) hydrogen bonds : angle 3.34617 ( 3144) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.92509 ( 72) covalent geometry : bond 0.00288 (17688) covalent geometry : angle 0.49918 (24060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9607.17 seconds wall clock time: 169 minutes 58.73 seconds (10198.73 seconds total)