Starting phenix.real_space_refine on Thu Mar 5 21:34:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k0b_9900/03_2026/6k0b_9900.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 682 5.49 5 S 38 5.16 5 C 13824 2.51 5 N 4656 2.21 5 O 6706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25908 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1920 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 4, 'TRANS': 226} Chain: "E" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1030 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "U" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1762 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 36, 'rna3p_pyr': 40} Link IDs: {'rna2p': 7, 'rna3p': 75} Chain: "X" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1920 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 4, 'TRANS': 226} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1030 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "V" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1762 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 36, 'rna3p_pyr': 40} Link IDs: {'rna2p': 7, 'rna3p': 75} Chain: "Y" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4310 SG CYS G 66 184.908 52.019 87.059 1.00126.46 S ATOM 4524 SG CYS G 92 188.441 51.798 89.370 1.00152.06 S ATOM 4547 SG CYS G 95 185.654 49.143 89.613 1.00153.71 S ATOM 17263 SG CYS H 66 66.193 109.284 86.901 1.00128.02 S ATOM 17477 SG CYS H 92 62.681 109.512 89.243 1.00149.50 S ATOM 17500 SG CYS H 95 65.471 112.168 89.452 1.00152.79 S Time building chain proxies: 5.37, per 1000 atoms: 0.21 Number of scatterers: 25908 At special positions: 0 Unit cell: (250.8, 162.36, 108.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 682 15.00 O 6706 8.00 N 4656 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 695.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 92 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 95 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 66 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 92 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 66 " 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.2% alpha, 15.4% beta 184 base pairs and 394 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 30 through 55 removed outlier: 9.169A pdb=" N SER A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TRP A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.707A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.502A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.628A pdb=" N ARG A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 removed outlier: 4.245A pdb=" N ILE C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 removed outlier: 4.009A pdb=" N TYR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.659A pdb=" N ALA C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 141 through 161 Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.611A pdb=" N VAL C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.610A pdb=" N MET C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 removed outlier: 3.897A pdb=" N LEU E 8 " --> pdb=" O HIS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.829A pdb=" N LYS E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 29 removed outlier: 3.709A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 removed outlier: 3.510A pdb=" N ALA G 36 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.654A pdb=" N GLN I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 41 Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.959A pdb=" N HIS I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 69 removed outlier: 3.783A pdb=" N LEU I 64 " --> pdb=" O HIS I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 86 removed outlier: 3.903A pdb=" N LEU I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'B' and resid 30 through 55 removed outlier: 9.168A pdb=" N SER B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TRP B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.706A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.502A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.628A pdb=" N ARG B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 removed outlier: 4.245A pdb=" N ILE D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 4.010A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 87 through 97 removed outlier: 3.658A pdb=" N ALA D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 141 through 161 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.611A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 217 removed outlier: 3.611A pdb=" N MET D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.897A pdb=" N LEU F 8 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.829A pdb=" N LYS F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 29 removed outlier: 3.708A pdb=" N LYS H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 51 removed outlier: 3.511A pdb=" N ALA H 36 " --> pdb=" O ASN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.654A pdb=" N GLN J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.958A pdb=" N HIS J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 69 removed outlier: 3.783A pdb=" N LEU J 64 " --> pdb=" O HIS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 86 removed outlier: 3.903A pdb=" N LEU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 111 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.707A pdb=" N TRP A 57 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 67 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 22 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N CYS A 97 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 24 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE A 95 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.411A pdb=" N ASP C 4 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 25 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY C 56 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE C 27 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LYS C 58 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ILE C 80 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N SER C 55 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N LEU C 82 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 57 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU C 84 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 59 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 81 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER C 104 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 83 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 103 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 223 through 225 removed outlier: 7.147A pdb=" N VAL E 60 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 16 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 34 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU E 45 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 36 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 76 through 81 Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 29 removed outlier: 3.900A pdb=" N LEU I 45 " --> pdb=" O ILE I 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.706A pdb=" N TRP B 57 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 67 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS B 22 " --> pdb=" O CYS B 97 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N CYS B 97 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 24 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE B 95 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.411A pdb=" N ASP D 4 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE D 25 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY D 56 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE D 27 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LYS D 58 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ILE D 80 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N SER D 55 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU D 82 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 57 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLU D 84 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 59 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE D 81 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER D 104 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 83 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 103 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 223 through 225 removed outlier: 7.147A pdb=" N VAL F 60 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS F 16 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL F 34 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU F 45 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP F 36 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 76 through 81 Processing sheet with id=AB1, first strand: chain 'J' and resid 27 through 29 removed outlier: 3.900A pdb=" N LEU J 45 " --> pdb=" O ILE J 96 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 490 hydrogen bonds 888 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 394 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4911 1.34 - 1.46: 9980 1.46 - 1.58: 11507 1.58 - 1.69: 1360 1.69 - 1.81: 56 Bond restraints: 27814 Sorted by residual: bond pdb=" C THR D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.332 1.358 -0.026 8.20e-03 1.49e+04 9.75e+00 bond pdb=" C THR C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.332 1.357 -0.025 8.20e-03 1.49e+04 8.93e+00 bond pdb=" C LEU I 61 " pdb=" N PRO I 62 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.00e+00 bond pdb=" C LEU J 61 " pdb=" N PRO J 62 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.69e+00 bond pdb=" N1 C X 47 " pdb=" C2 C X 47 " ideal model delta sigma weight residual 1.397 1.424 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 27809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 39866 2.18 - 4.35: 830 4.35 - 6.53: 111 6.53 - 8.70: 19 8.70 - 10.88: 6 Bond angle restraints: 40832 Sorted by residual: angle pdb=" C ILE C 226 " pdb=" N ILE C 227 " pdb=" CA ILE C 227 " ideal model delta sigma weight residual 121.97 131.32 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C ILE D 226 " pdb=" N ILE D 227 " pdb=" CA ILE D 227 " ideal model delta sigma weight residual 121.97 131.29 -9.32 1.80e+00 3.09e-01 2.68e+01 angle pdb=" C LEU D 97 " pdb=" N HIS D 98 " pdb=" CA HIS D 98 " ideal model delta sigma weight residual 122.07 128.61 -6.54 1.43e+00 4.89e-01 2.09e+01 angle pdb=" C LEU C 97 " pdb=" N HIS C 98 " pdb=" CA HIS C 98 " ideal model delta sigma weight residual 122.07 128.57 -6.50 1.43e+00 4.89e-01 2.07e+01 angle pdb=" N LEU C 51 " pdb=" CA LEU C 51 " pdb=" C LEU C 51 " ideal model delta sigma weight residual 108.60 114.15 -5.55 1.46e+00 4.69e-01 1.44e+01 ... (remaining 40827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 15926 34.82 - 69.64: 1736 69.64 - 104.46: 238 104.46 - 139.28: 0 139.28 - 174.10: 4 Dihedral angle restraints: 17904 sinusoidal: 13850 harmonic: 4054 Sorted by residual: dihedral pdb=" O4' U X 207 " pdb=" C1' U X 207 " pdb=" N1 U X 207 " pdb=" C2 U X 207 " ideal model delta sinusoidal sigma weight residual 232.00 57.90 174.10 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U Y 207 " pdb=" C1' U Y 207 " pdb=" N1 U Y 207 " pdb=" C2 U Y 207 " ideal model delta sinusoidal sigma weight residual 232.00 57.94 174.06 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4591 0.061 - 0.123: 461 0.123 - 0.184: 67 0.184 - 0.246: 9 0.246 - 0.307: 2 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE D 226 " pdb=" CA ILE D 226 " pdb=" CG1 ILE D 226 " pdb=" CG2 ILE D 226 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE B 96 " pdb=" CA ILE B 96 " pdb=" CG1 ILE B 96 " pdb=" CG2 ILE B 96 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 5127 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 64 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 63 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO B 64 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 46 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C TYR A 46 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR A 46 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 47 " -0.018 2.00e-02 2.50e+03 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 180 2.59 - 3.17: 18151 3.17 - 3.74: 45194 3.74 - 4.32: 61929 4.32 - 4.90: 87519 Nonbonded interactions: 212973 Sorted by model distance: nonbonded pdb=" OG1 THR E 41 " pdb=" OP1 A X 75 " model vdw 2.011 3.040 nonbonded pdb=" NZ LYS G 114 " pdb=" OP1 G X 125 " model vdw 2.077 3.120 nonbonded pdb=" NH2 ARG H 60 " pdb=" OP1 U Y 161 " model vdw 2.100 3.120 nonbonded pdb=" OG1 THR F 41 " pdb=" OP1 A Y 75 " model vdw 2.120 3.040 nonbonded pdb=" N2 G Y 223 " pdb=" OP2 A Y 226 " model vdw 2.153 3.120 ... (remaining 212968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.450 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.005 0.283 27820 Z= 0.223 Angle : 0.777 10.877 40832 Z= 0.423 Chirality : 0.038 0.307 5130 Planarity : 0.006 0.086 2588 Dihedral : 22.118 174.099 15280 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.66 % Allowed : 2.46 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.18), residues: 1356 helix: -2.65 (0.15), residues: 610 sheet: -1.03 (0.35), residues: 192 loop : -2.54 (0.22), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 153 TYR 0.030 0.003 TYR B 25 PHE 0.035 0.004 PHE D 152 TRP 0.020 0.002 TRP B 120 HIS 0.008 0.002 HIS E 10 Details of bonding type rmsd covalent geometry : bond 0.00322 (27814) covalent geometry : angle 0.77654 (40832) hydrogen bonds : bond 0.14339 ( 992) hydrogen bonds : angle 6.63199 ( 2364) metal coordination : bond 0.26445 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 723 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8375 (pp) cc_final: 0.8051 (pp) REVERT: A 53 LYS cc_start: 0.8035 (tttt) cc_final: 0.7093 (ttpt) REVERT: A 65 TYR cc_start: 0.7395 (m-80) cc_final: 0.6816 (m-10) REVERT: A 76 ASP cc_start: 0.8421 (m-30) cc_final: 0.8075 (m-30) REVERT: C 32 ASP cc_start: 0.8374 (m-30) cc_final: 0.7958 (p0) REVERT: C 40 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8717 (tm-30) REVERT: C 47 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 63 SER cc_start: 0.8390 (m) cc_final: 0.7984 (p) REVERT: C 70 LYS cc_start: 0.8994 (mttt) cc_final: 0.8758 (ptpt) REVERT: C 96 GLU cc_start: 0.8497 (tt0) cc_final: 0.8107 (tp30) REVERT: C 105 THR cc_start: 0.7575 (m) cc_final: 0.7277 (m) REVERT: C 134 PHE cc_start: 0.6657 (t80) cc_final: 0.6326 (t80) REVERT: C 150 LEU cc_start: 0.9345 (tp) cc_final: 0.9064 (tp) REVERT: C 167 VAL cc_start: 0.8559 (t) cc_final: 0.7908 (p) REVERT: E 20 VAL cc_start: 0.8958 (p) cc_final: 0.8298 (m) REVERT: E 85 LEU cc_start: 0.9302 (tp) cc_final: 0.9098 (tt) REVERT: G 90 ILE cc_start: 0.9108 (mm) cc_final: 0.8889 (pt) REVERT: I 47 ILE cc_start: 0.9150 (mp) cc_final: 0.8820 (tp) REVERT: I 56 GLU cc_start: 0.9022 (mp0) cc_final: 0.8819 (mm-30) REVERT: B 23 ILE cc_start: 0.7822 (mt) cc_final: 0.7537 (mt) REVERT: B 37 LEU cc_start: 0.8593 (pp) cc_final: 0.8311 (pp) REVERT: B 43 LEU cc_start: 0.8042 (tt) cc_final: 0.7722 (tt) REVERT: B 53 LYS cc_start: 0.7673 (tttt) cc_final: 0.6883 (ttpt) REVERT: B 65 TYR cc_start: 0.7225 (m-80) cc_final: 0.6573 (m-80) REVERT: B 76 ASP cc_start: 0.8451 (m-30) cc_final: 0.8148 (m-30) REVERT: D 32 ASP cc_start: 0.8289 (m-30) cc_final: 0.8036 (p0) REVERT: D 63 SER cc_start: 0.8344 (m) cc_final: 0.7913 (p) REVERT: D 70 LYS cc_start: 0.9084 (mttt) cc_final: 0.8749 (ptpt) REVERT: D 74 PHE cc_start: 0.8336 (m-80) cc_final: 0.8133 (m-80) REVERT: D 96 GLU cc_start: 0.8459 (tt0) cc_final: 0.8200 (tp30) REVERT: D 105 THR cc_start: 0.7701 (m) cc_final: 0.7108 (m) REVERT: D 134 PHE cc_start: 0.6730 (t80) cc_final: 0.6484 (t80) REVERT: D 167 VAL cc_start: 0.8695 (t) cc_final: 0.7870 (p) REVERT: F 20 VAL cc_start: 0.8862 (p) cc_final: 0.7930 (m) REVERT: F 58 ILE cc_start: 0.8426 (tt) cc_final: 0.8138 (mm) REVERT: H 12 ILE cc_start: 0.9430 (mm) cc_final: 0.9050 (tt) REVERT: H 17 ILE cc_start: 0.9080 (mm) cc_final: 0.8868 (mm) REVERT: H 23 LEU cc_start: 0.9665 (mt) cc_final: 0.9026 (mm) REVERT: H 68 THR cc_start: 0.8312 (m) cc_final: 0.8002 (t) REVERT: H 108 LYS cc_start: 0.8742 (mttt) cc_final: 0.8473 (tptt) REVERT: J 47 ILE cc_start: 0.8934 (mp) cc_final: 0.8559 (tp) outliers start: 8 outliers final: 2 residues processed: 725 average time/residue: 0.2049 time to fit residues: 219.3584 Evaluate side-chains 362 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 180 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 155 ASN D 180 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.093275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.073629 restraints weight = 169380.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.075333 restraints weight = 94421.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.076517 restraints weight = 64545.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077248 restraints weight = 51181.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.077689 restraints weight = 44642.674| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27820 Z= 0.157 Angle : 0.640 9.531 40832 Z= 0.328 Chirality : 0.035 0.266 5130 Planarity : 0.006 0.069 2588 Dihedral : 23.731 178.230 12238 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.21), residues: 1356 helix: -0.92 (0.20), residues: 618 sheet: -0.70 (0.33), residues: 238 loop : -2.24 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 105 TYR 0.029 0.002 TYR D 176 PHE 0.016 0.002 PHE F 61 TRP 0.012 0.002 TRP H 58 HIS 0.004 0.001 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00335 (27814) covalent geometry : angle 0.63993 (40832) hydrogen bonds : bond 0.05280 ( 992) hydrogen bonds : angle 4.21648 ( 2364) metal coordination : bond 0.00218 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 445 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7828 (m-80) cc_final: 0.7424 (m-10) REVERT: A 76 ASP cc_start: 0.8761 (m-30) cc_final: 0.8521 (m-30) REVERT: A 82 LEU cc_start: 0.8703 (mt) cc_final: 0.8490 (mt) REVERT: C 7 ARG cc_start: 0.8179 (ptp-170) cc_final: 0.7873 (mtt180) REVERT: C 63 SER cc_start: 0.8548 (m) cc_final: 0.7992 (p) REVERT: C 97 LEU cc_start: 0.8818 (pp) cc_final: 0.8385 (mt) REVERT: C 107 GLU cc_start: 0.6899 (pm20) cc_final: 0.6247 (tm-30) REVERT: C 213 TYR cc_start: 0.7929 (t80) cc_final: 0.7672 (t80) REVERT: C 221 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7644 (mtp180) REVERT: E 12 LEU cc_start: 0.9122 (mt) cc_final: 0.8475 (tp) REVERT: E 13 ILE cc_start: 0.9636 (mt) cc_final: 0.9436 (mt) REVERT: E 82 GLU cc_start: 0.8600 (mp0) cc_final: 0.8316 (pm20) REVERT: E 90 LYS cc_start: 0.7984 (tppt) cc_final: 0.7622 (tppt) REVERT: G 12 ILE cc_start: 0.9780 (tt) cc_final: 0.8213 (tt) REVERT: G 17 ILE cc_start: 0.9409 (mm) cc_final: 0.9144 (mm) REVERT: G 25 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7885 (mt-10) REVERT: G 93 LEU cc_start: 0.8766 (mm) cc_final: 0.8357 (mt) REVERT: G 109 GLU cc_start: 0.9171 (tp30) cc_final: 0.8852 (tp30) REVERT: I 72 TYR cc_start: 0.8702 (p90) cc_final: 0.8233 (p90) REVERT: I 79 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8472 (pm20) REVERT: I 97 ILE cc_start: 0.7619 (pt) cc_final: 0.7384 (pt) REVERT: I 110 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9233 (pp20) REVERT: B 44 GLU cc_start: 0.8091 (tp30) cc_final: 0.7737 (tp30) REVERT: B 49 TRP cc_start: 0.9310 (t60) cc_final: 0.9108 (t60) REVERT: B 53 LYS cc_start: 0.8216 (tttt) cc_final: 0.7244 (ttpt) REVERT: B 65 TYR cc_start: 0.7619 (m-80) cc_final: 0.7173 (m-10) REVERT: D 7 ARG cc_start: 0.8193 (ptp-170) cc_final: 0.7628 (mtt180) REVERT: D 37 ASP cc_start: 0.8987 (p0) cc_final: 0.8354 (p0) REVERT: D 74 PHE cc_start: 0.8544 (m-80) cc_final: 0.8232 (m-10) REVERT: D 96 GLU cc_start: 0.8680 (tt0) cc_final: 0.8208 (tp30) REVERT: D 97 LEU cc_start: 0.8708 (pp) cc_final: 0.8462 (mt) REVERT: D 179 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8376 (mmmt) REVERT: F 12 LEU cc_start: 0.9063 (mt) cc_final: 0.8187 (tp) REVERT: F 82 GLU cc_start: 0.8558 (mp0) cc_final: 0.8169 (pm20) REVERT: H 85 TYR cc_start: 0.8188 (p90) cc_final: 0.7660 (p90) REVERT: H 94 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8148 (mp0) REVERT: H 108 LYS cc_start: 0.8803 (mttt) cc_final: 0.8370 (tppt) REVERT: J 72 TYR cc_start: 0.8595 (p90) cc_final: 0.8226 (p90) outliers start: 3 outliers final: 1 residues processed: 447 average time/residue: 0.1868 time to fit residues: 127.4926 Evaluate side-chains 331 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN I 14 GLN B 36 ASN D 155 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.085541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064879 restraints weight = 169224.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066426 restraints weight = 91271.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 80)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067544 restraints weight = 62542.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.068190 restraints weight = 50133.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.068590 restraints weight = 44310.388| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 27820 Z= 0.228 Angle : 0.722 11.838 40832 Z= 0.367 Chirality : 0.037 0.251 5130 Planarity : 0.006 0.068 2588 Dihedral : 23.800 179.920 12238 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.33 % Allowed : 7.14 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1356 helix: -0.20 (0.21), residues: 600 sheet: -0.81 (0.34), residues: 220 loop : -1.75 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 111 TYR 0.021 0.003 TYR E 95 PHE 0.020 0.003 PHE D 152 TRP 0.028 0.003 TRP A 57 HIS 0.004 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00483 (27814) covalent geometry : angle 0.72205 (40832) hydrogen bonds : bond 0.06824 ( 992) hydrogen bonds : angle 4.26983 ( 2364) metal coordination : bond 0.00243 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 409 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9431 (tp) cc_final: 0.9204 (tt) REVERT: A 65 TYR cc_start: 0.8195 (m-80) cc_final: 0.7811 (m-10) REVERT: C 21 LYS cc_start: 0.7376 (mmmt) cc_final: 0.6645 (tmtt) REVERT: C 27 PHE cc_start: 0.7670 (t80) cc_final: 0.7392 (t80) REVERT: C 40 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8969 (tm-30) REVERT: C 74 PHE cc_start: 0.8351 (m-80) cc_final: 0.7644 (m-80) REVERT: C 82 LEU cc_start: 0.9102 (tp) cc_final: 0.8755 (tp) REVERT: E 82 GLU cc_start: 0.8627 (mp0) cc_final: 0.8343 (pm20) REVERT: E 83 GLU cc_start: 0.8981 (pm20) cc_final: 0.8749 (pm20) REVERT: G 12 ILE cc_start: 0.9482 (tt) cc_final: 0.9213 (tt) REVERT: G 15 GLU cc_start: 0.8906 (tp30) cc_final: 0.8667 (tp30) REVERT: G 25 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7891 (mt-10) REVERT: G 64 LYS cc_start: 0.9442 (mttt) cc_final: 0.9185 (mmmt) REVERT: I 72 TYR cc_start: 0.8728 (p90) cc_final: 0.8200 (p90) REVERT: B 48 SER cc_start: 0.9125 (m) cc_final: 0.8695 (t) REVERT: B 71 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7357 (tm-30) REVERT: B 87 GLU cc_start: 0.8133 (tp30) cc_final: 0.7829 (mm-30) REVERT: D 80 ILE cc_start: 0.9215 (pt) cc_final: 0.8840 (pt) REVERT: F 12 LEU cc_start: 0.9190 (mt) cc_final: 0.8570 (tp) REVERT: F 21 GLU cc_start: 0.7636 (mp0) cc_final: 0.7393 (mp0) REVERT: F 57 ASP cc_start: 0.8921 (p0) cc_final: 0.8580 (p0) REVERT: H 15 GLU cc_start: 0.8929 (tp30) cc_final: 0.8570 (tp30) REVERT: H 17 ILE cc_start: 0.9324 (mm) cc_final: 0.9067 (mm) REVERT: H 108 LYS cc_start: 0.9047 (mttt) cc_final: 0.8819 (tptt) REVERT: J 11 GLU cc_start: 0.8679 (tp30) cc_final: 0.8300 (tp30) REVERT: J 45 LEU cc_start: 0.8435 (tp) cc_final: 0.8209 (tp) REVERT: J 72 TYR cc_start: 0.8578 (p90) cc_final: 0.8129 (p90) outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.1555 time to fit residues: 103.1676 Evaluate side-chains 293 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 8 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 153 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.087713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.067196 restraints weight = 170235.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.068726 restraints weight = 92677.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.069848 restraints weight = 64129.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.070562 restraints weight = 51569.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.070954 restraints weight = 45621.272| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27820 Z= 0.117 Angle : 0.578 8.555 40832 Z= 0.295 Chirality : 0.033 0.207 5130 Planarity : 0.005 0.059 2588 Dihedral : 23.620 178.035 12238 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1356 helix: 0.21 (0.21), residues: 594 sheet: -0.60 (0.34), residues: 232 loop : -1.62 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 75 TYR 0.028 0.002 TYR B 25 PHE 0.021 0.002 PHE D 152 TRP 0.020 0.002 TRP H 58 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00245 (27814) covalent geometry : angle 0.57757 (40832) hydrogen bonds : bond 0.04536 ( 992) hydrogen bonds : angle 3.92290 ( 2364) metal coordination : bond 0.00048 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7708 (m-80) cc_final: 0.7211 (m-10) REVERT: A 71 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 76 ASP cc_start: 0.8867 (m-30) cc_final: 0.8664 (m-30) REVERT: C 40 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8924 (tm-30) REVERT: C 74 PHE cc_start: 0.8262 (m-80) cc_final: 0.7568 (m-80) REVERT: C 121 ARG cc_start: 0.8970 (mmm160) cc_final: 0.8618 (tpp80) REVERT: E 20 VAL cc_start: 0.8568 (m) cc_final: 0.8296 (m) REVERT: E 83 GLU cc_start: 0.8788 (pm20) cc_final: 0.8334 (pm20) REVERT: G 17 ILE cc_start: 0.9437 (mm) cc_final: 0.9127 (mm) REVERT: G 18 ASP cc_start: 0.9055 (m-30) cc_final: 0.8842 (m-30) REVERT: G 25 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7917 (mt-10) REVERT: G 64 LYS cc_start: 0.9429 (mttt) cc_final: 0.8883 (mmmm) REVERT: G 93 LEU cc_start: 0.8959 (mm) cc_final: 0.8627 (mt) REVERT: I 72 TYR cc_start: 0.8621 (p90) cc_final: 0.8157 (p90) REVERT: I 77 SER cc_start: 0.8306 (t) cc_final: 0.7854 (t) REVERT: B 36 ASN cc_start: 0.7919 (m-40) cc_final: 0.7487 (m-40) REVERT: B 48 SER cc_start: 0.8922 (m) cc_final: 0.8350 (t) REVERT: B 61 TYR cc_start: 0.6314 (t80) cc_final: 0.5886 (t80) REVERT: B 71 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 76 ASP cc_start: 0.8887 (m-30) cc_final: 0.8599 (m-30) REVERT: B 95 ILE cc_start: 0.9016 (mm) cc_final: 0.8806 (mm) REVERT: D 37 ASP cc_start: 0.8890 (p0) cc_final: 0.8670 (p0) REVERT: D 74 PHE cc_start: 0.8335 (m-80) cc_final: 0.7561 (m-80) REVERT: D 158 LEU cc_start: 0.9532 (tt) cc_final: 0.9309 (tp) REVERT: D 196 TYR cc_start: 0.8484 (t80) cc_final: 0.8278 (t80) REVERT: F 12 LEU cc_start: 0.9154 (mt) cc_final: 0.8671 (tp) REVERT: F 57 ASP cc_start: 0.8917 (p0) cc_final: 0.8578 (p0) REVERT: F 62 LEU cc_start: 0.8946 (tp) cc_final: 0.8544 (tp) REVERT: H 17 ILE cc_start: 0.9288 (mm) cc_final: 0.9041 (mm) REVERT: H 48 MET cc_start: 0.8771 (mmm) cc_final: 0.7580 (tpp) REVERT: H 108 LYS cc_start: 0.9041 (mttt) cc_final: 0.8625 (tppt) REVERT: J 72 TYR cc_start: 0.8393 (p90) cc_final: 0.8117 (p90) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1590 time to fit residues: 100.3358 Evaluate side-chains 312 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 102 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 74 ASN C 154 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.086343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.065526 restraints weight = 168891.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.066995 restraints weight = 94829.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.068116 restraints weight = 65338.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.068736 restraints weight = 52563.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.069188 restraints weight = 46503.460| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27820 Z= 0.125 Angle : 0.573 8.574 40832 Z= 0.294 Chirality : 0.033 0.255 5130 Planarity : 0.005 0.058 2588 Dihedral : 23.516 179.031 12238 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1356 helix: 0.45 (0.21), residues: 594 sheet: -0.42 (0.35), residues: 228 loop : -1.60 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 45 TYR 0.032 0.002 TYR C 176 PHE 0.011 0.002 PHE B 111 TRP 0.019 0.002 TRP H 58 HIS 0.003 0.001 HIS E 10 Details of bonding type rmsd covalent geometry : bond 0.00261 (27814) covalent geometry : angle 0.57276 (40832) hydrogen bonds : bond 0.04573 ( 992) hydrogen bonds : angle 3.79360 ( 2364) metal coordination : bond 0.00188 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.9163 (p) cc_final: 0.8738 (t) REVERT: A 14 GLU cc_start: 0.8418 (pp20) cc_final: 0.7997 (pp20) REVERT: A 65 TYR cc_start: 0.7540 (m-80) cc_final: 0.7176 (m-10) REVERT: A 71 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 84 LEU cc_start: 0.9000 (mm) cc_final: 0.8700 (tp) REVERT: C 21 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6376 (tmtt) REVERT: C 40 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8837 (tm-30) REVERT: C 74 PHE cc_start: 0.8170 (m-10) cc_final: 0.7511 (m-80) REVERT: E 18 GLU cc_start: 0.7833 (tp30) cc_final: 0.7510 (tp30) REVERT: E 20 VAL cc_start: 0.8478 (m) cc_final: 0.7981 (m) REVERT: E 73 ASP cc_start: 0.8534 (t0) cc_final: 0.8022 (t0) REVERT: E 83 GLU cc_start: 0.8742 (pm20) cc_final: 0.8415 (pm20) REVERT: E 92 LEU cc_start: 0.9179 (mp) cc_final: 0.8674 (mp) REVERT: G 25 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7860 (mt-10) REVERT: G 64 LYS cc_start: 0.9385 (mttt) cc_final: 0.8982 (mmmm) REVERT: G 93 LEU cc_start: 0.8934 (mm) cc_final: 0.8689 (mt) REVERT: I 45 LEU cc_start: 0.8175 (tp) cc_final: 0.7943 (tp) REVERT: I 72 TYR cc_start: 0.8394 (p90) cc_final: 0.8105 (p90) REVERT: B 48 SER cc_start: 0.8825 (m) cc_final: 0.8406 (t) REVERT: B 76 ASP cc_start: 0.8670 (m-30) cc_final: 0.8427 (m-30) REVERT: B 95 ILE cc_start: 0.8976 (mm) cc_final: 0.8728 (mm) REVERT: D 37 ASP cc_start: 0.8977 (p0) cc_final: 0.8479 (p0) REVERT: D 74 PHE cc_start: 0.8256 (m-80) cc_final: 0.7518 (m-80) REVERT: D 196 TYR cc_start: 0.8536 (t80) cc_final: 0.8224 (t80) REVERT: F 18 GLU cc_start: 0.8124 (tp30) cc_final: 0.7816 (tp30) REVERT: F 62 LEU cc_start: 0.9097 (tp) cc_final: 0.8612 (tp) REVERT: H 3 LYS cc_start: 0.4676 (mttt) cc_final: 0.3724 (mttp) REVERT: H 17 ILE cc_start: 0.9156 (mm) cc_final: 0.8914 (mm) REVERT: H 108 LYS cc_start: 0.9120 (mttt) cc_final: 0.8708 (tppt) REVERT: J 45 LEU cc_start: 0.8070 (tp) cc_final: 0.7817 (tp) REVERT: J 72 TYR cc_start: 0.8233 (p90) cc_final: 0.7966 (p90) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.1573 time to fit residues: 98.2281 Evaluate side-chains 297 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 174 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN D 29 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.079928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.058565 restraints weight = 169083.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060157 restraints weight = 90643.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061233 restraints weight = 62357.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061847 restraints weight = 50316.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062213 restraints weight = 44759.622| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27820 Z= 0.261 Angle : 0.744 11.760 40832 Z= 0.379 Chirality : 0.039 0.240 5130 Planarity : 0.006 0.062 2588 Dihedral : 23.887 178.961 12238 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1356 helix: 0.07 (0.20), residues: 604 sheet: -0.29 (0.35), residues: 228 loop : -1.58 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 153 TYR 0.019 0.003 TYR D 176 PHE 0.023 0.003 PHE D 152 TRP 0.021 0.003 TRP D 22 HIS 0.007 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00534 (27814) covalent geometry : angle 0.74393 (40832) hydrogen bonds : bond 0.07545 ( 992) hydrogen bonds : angle 4.24871 ( 2364) metal coordination : bond 0.00406 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8560 (pp20) cc_final: 0.8279 (pp20) REVERT: A 34 VAL cc_start: 0.9041 (t) cc_final: 0.8732 (t) REVERT: A 48 SER cc_start: 0.8606 (m) cc_final: 0.8244 (t) REVERT: A 71 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8489 (tm-30) REVERT: C 21 LYS cc_start: 0.7470 (mmmt) cc_final: 0.6749 (tmtt) REVERT: C 40 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9019 (tm-30) REVERT: C 74 PHE cc_start: 0.8658 (m-80) cc_final: 0.7887 (m-80) REVERT: C 154 ASN cc_start: 0.8774 (m-40) cc_final: 0.8570 (m-40) REVERT: E 20 VAL cc_start: 0.8769 (m) cc_final: 0.8409 (m) REVERT: E 73 ASP cc_start: 0.8485 (t0) cc_final: 0.8091 (t0) REVERT: E 83 GLU cc_start: 0.9042 (pm20) cc_final: 0.8596 (pm20) REVERT: G 15 GLU cc_start: 0.9012 (tp30) cc_final: 0.8737 (tp30) REVERT: G 18 ASP cc_start: 0.9059 (m-30) cc_final: 0.8707 (m-30) REVERT: G 25 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8045 (mt-10) REVERT: I 45 LEU cc_start: 0.8771 (tp) cc_final: 0.8501 (tp) REVERT: I 60 HIS cc_start: 0.8132 (p-80) cc_final: 0.7912 (p-80) REVERT: I 72 TYR cc_start: 0.8696 (p90) cc_final: 0.8053 (p90) REVERT: B 48 SER cc_start: 0.8748 (m) cc_final: 0.8265 (t) REVERT: B 71 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7690 (tm-30) REVERT: D 37 ASP cc_start: 0.9115 (p0) cc_final: 0.8754 (p0) REVERT: D 47 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8363 (mm-30) REVERT: D 74 PHE cc_start: 0.8785 (m-80) cc_final: 0.7827 (m-80) REVERT: F 18 GLU cc_start: 0.8105 (tp30) cc_final: 0.7615 (tp30) REVERT: F 27 MET cc_start: 0.9065 (mtm) cc_final: 0.8834 (mmm) REVERT: F 73 ASP cc_start: 0.8550 (t0) cc_final: 0.7744 (t0) REVERT: H 3 LYS cc_start: 0.4477 (mttt) cc_final: 0.3791 (mttp) REVERT: H 15 GLU cc_start: 0.8860 (tp30) cc_final: 0.8544 (tp30) REVERT: H 108 LYS cc_start: 0.9404 (mttt) cc_final: 0.8934 (tppt) REVERT: J 45 LEU cc_start: 0.8710 (tp) cc_final: 0.8374 (tp) REVERT: J 72 TYR cc_start: 0.8635 (p90) cc_final: 0.8197 (p90) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1500 time to fit residues: 85.8003 Evaluate side-chains 261 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 131 optimal weight: 0.6980 chunk 111 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 155 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.083780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.062815 restraints weight = 175501.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064284 restraints weight = 98184.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.065462 restraints weight = 69539.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.066098 restraints weight = 56799.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066467 restraints weight = 50754.498| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27820 Z= 0.122 Angle : 0.603 8.437 40832 Z= 0.308 Chirality : 0.035 0.202 5130 Planarity : 0.005 0.063 2588 Dihedral : 23.650 177.598 12238 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.16 % Allowed : 1.97 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1356 helix: 0.44 (0.21), residues: 592 sheet: -0.37 (0.34), residues: 246 loop : -1.54 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 7 TYR 0.035 0.002 TYR F 93 PHE 0.017 0.002 PHE C 152 TRP 0.019 0.002 TRP H 58 HIS 0.008 0.001 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00256 (27814) covalent geometry : angle 0.60283 (40832) hydrogen bonds : bond 0.04350 ( 992) hydrogen bonds : angle 3.87383 ( 2364) metal coordination : bond 0.00092 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8745 (pp20) cc_final: 0.8041 (pp20) REVERT: A 48 SER cc_start: 0.8456 (m) cc_final: 0.7943 (t) REVERT: A 71 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 21 LYS cc_start: 0.7477 (mmmt) cc_final: 0.6760 (tmtt) REVERT: C 40 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8954 (tm-30) REVERT: C 74 PHE cc_start: 0.8398 (m-10) cc_final: 0.7683 (m-80) REVERT: C 171 ASP cc_start: 0.8230 (t70) cc_final: 0.7887 (t70) REVERT: E 20 VAL cc_start: 0.8367 (m) cc_final: 0.8092 (m) REVERT: G 15 GLU cc_start: 0.8893 (tp30) cc_final: 0.8641 (tp30) REVERT: G 18 ASP cc_start: 0.9039 (m-30) cc_final: 0.8707 (m-30) REVERT: G 25 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7770 (mt-10) REVERT: G 48 MET cc_start: 0.8505 (mmm) cc_final: 0.7899 (tpt) REVERT: G 93 LEU cc_start: 0.9170 (mm) cc_final: 0.8895 (mt) REVERT: G 116 GLU cc_start: 0.9205 (pt0) cc_final: 0.8602 (pt0) REVERT: I 45 LEU cc_start: 0.8749 (tp) cc_final: 0.8458 (tp) REVERT: I 55 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6506 (mm-30) REVERT: I 72 TYR cc_start: 0.8533 (p90) cc_final: 0.8008 (p90) REVERT: B 48 SER cc_start: 0.8705 (m) cc_final: 0.8145 (t) REVERT: B 71 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 76 ASP cc_start: 0.8750 (m-30) cc_final: 0.8433 (m-30) REVERT: B 77 TYR cc_start: 0.8080 (m-10) cc_final: 0.7874 (m-10) REVERT: D 37 ASP cc_start: 0.9055 (p0) cc_final: 0.8542 (p0) REVERT: D 177 GLN cc_start: 0.8283 (tp40) cc_final: 0.7719 (tp40) REVERT: D 179 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8570 (mmtt) REVERT: D 187 PHE cc_start: 0.9135 (t80) cc_final: 0.8914 (t80) REVERT: F 62 LEU cc_start: 0.9191 (tp) cc_final: 0.8978 (tp) REVERT: H 3 LYS cc_start: 0.4366 (mttt) cc_final: 0.3954 (tptm) REVERT: H 15 GLU cc_start: 0.8849 (tp30) cc_final: 0.8629 (tp30) REVERT: H 48 MET cc_start: 0.8498 (mmm) cc_final: 0.7897 (tpp) REVERT: H 50 MET cc_start: 0.8936 (mmm) cc_final: 0.8728 (mmp) REVERT: H 85 TYR cc_start: 0.8640 (p90) cc_final: 0.8179 (p90) REVERT: H 108 LYS cc_start: 0.9285 (mttt) cc_final: 0.8991 (tppt) REVERT: H 115 LEU cc_start: 0.8792 (mt) cc_final: 0.8525 (mt) REVERT: J 45 LEU cc_start: 0.8523 (tp) cc_final: 0.8260 (tp) outliers start: 2 outliers final: 1 residues processed: 375 average time/residue: 0.1578 time to fit residues: 96.6030 Evaluate side-chains 275 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 170 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.080823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060690 restraints weight = 176714.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061949 restraints weight = 103830.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062577 restraints weight = 77081.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062994 restraints weight = 58019.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.062994 restraints weight = 53781.972| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27820 Z= 0.197 Angle : 0.656 9.580 40832 Z= 0.338 Chirality : 0.036 0.204 5130 Planarity : 0.005 0.061 2588 Dihedral : 23.692 179.183 12238 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.52 % Favored : 92.40 % Rotamer: Outliers : 0.08 % Allowed : 1.97 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1356 helix: 0.45 (0.21), residues: 590 sheet: -0.34 (0.34), residues: 242 loop : -1.50 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 112 TYR 0.037 0.002 TYR C 196 PHE 0.020 0.002 PHE C 152 TRP 0.037 0.002 TRP H 58 HIS 0.008 0.001 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00406 (27814) covalent geometry : angle 0.65610 (40832) hydrogen bonds : bond 0.05848 ( 992) hydrogen bonds : angle 4.03407 ( 2364) metal coordination : bond 0.00295 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8652 (m) cc_final: 0.8144 (t) REVERT: A 71 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 21 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6737 (tmtt) REVERT: C 40 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9043 (tm-30) REVERT: C 68 ARG cc_start: 0.8825 (ptm160) cc_final: 0.8604 (ptp-170) REVERT: C 74 PHE cc_start: 0.8648 (m-10) cc_final: 0.7906 (m-80) REVERT: C 154 ASN cc_start: 0.8753 (m-40) cc_final: 0.8533 (m-40) REVERT: E 6 ASN cc_start: 0.9169 (t0) cc_final: 0.8869 (t0) REVERT: G 15 GLU cc_start: 0.8911 (tp30) cc_final: 0.8633 (tp30) REVERT: G 18 ASP cc_start: 0.9003 (m-30) cc_final: 0.8737 (m-30) REVERT: G 25 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8014 (mt-10) REVERT: G 50 MET cc_start: 0.8796 (mmp) cc_final: 0.8533 (mmp) REVERT: G 93 LEU cc_start: 0.9244 (mm) cc_final: 0.8903 (mp) REVERT: I 45 LEU cc_start: 0.8863 (tp) cc_final: 0.8522 (tp) REVERT: I 55 GLU cc_start: 0.7782 (mm-30) cc_final: 0.6840 (mm-30) REVERT: I 72 TYR cc_start: 0.8643 (p90) cc_final: 0.7958 (p90) REVERT: B 48 SER cc_start: 0.8720 (m) cc_final: 0.8182 (t) REVERT: B 71 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 37 ASP cc_start: 0.9204 (p0) cc_final: 0.8845 (p0) REVERT: F 8 LEU cc_start: 0.9003 (mm) cc_final: 0.8768 (tp) REVERT: H 3 LYS cc_start: 0.4399 (mttt) cc_final: 0.4071 (tptm) REVERT: H 15 GLU cc_start: 0.8852 (tp30) cc_final: 0.8542 (tp30) REVERT: H 48 MET cc_start: 0.8589 (mmm) cc_final: 0.7910 (tpp) REVERT: H 85 TYR cc_start: 0.8426 (p90) cc_final: 0.8052 (p90) REVERT: H 108 LYS cc_start: 0.9340 (mttt) cc_final: 0.8978 (tppt) REVERT: H 112 ARG cc_start: 0.9362 (pmt-80) cc_final: 0.8632 (mmp-170) REVERT: J 45 LEU cc_start: 0.8676 (tp) cc_final: 0.8339 (tp) REVERT: J 72 TYR cc_start: 0.8560 (p90) cc_final: 0.8176 (p90) REVERT: J 81 LEU cc_start: 0.9765 (mt) cc_final: 0.9473 (mt) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.1469 time to fit residues: 81.3715 Evaluate side-chains 263 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 36 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 131 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN J 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.081617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061928 restraints weight = 173375.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063343 restraints weight = 106782.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063908 restraints weight = 67290.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063989 restraints weight = 55678.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.064026 restraints weight = 54333.865| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27820 Z= 0.142 Angle : 0.616 9.937 40832 Z= 0.316 Chirality : 0.035 0.186 5130 Planarity : 0.004 0.059 2588 Dihedral : 23.635 177.612 12238 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.08 % Allowed : 0.57 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.23), residues: 1356 helix: 0.35 (0.21), residues: 600 sheet: -0.23 (0.34), residues: 238 loop : -1.58 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 112 TYR 0.022 0.002 TYR C 213 PHE 0.019 0.002 PHE E 63 TRP 0.026 0.002 TRP H 58 HIS 0.008 0.001 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00297 (27814) covalent geometry : angle 0.61608 (40832) hydrogen bonds : bond 0.04682 ( 992) hydrogen bonds : angle 3.93671 ( 2364) metal coordination : bond 0.00135 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8768 (pp20) cc_final: 0.8104 (pp20) REVERT: A 48 SER cc_start: 0.8434 (m) cc_final: 0.7935 (t) REVERT: A 58 LEU cc_start: 0.9063 (tt) cc_final: 0.8839 (mm) REVERT: A 60 TYR cc_start: 0.7255 (t80) cc_final: 0.7054 (t80) REVERT: A 71 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 21 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6695 (tmtt) REVERT: C 40 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8995 (tm-30) REVERT: C 74 PHE cc_start: 0.8408 (m-10) cc_final: 0.7733 (m-80) REVERT: C 154 ASN cc_start: 0.8722 (m-40) cc_final: 0.8516 (m-40) REVERT: C 171 ASP cc_start: 0.8142 (t70) cc_final: 0.7847 (t70) REVERT: C 179 LYS cc_start: 0.8678 (mmpt) cc_final: 0.8390 (mmpt) REVERT: E 6 ASN cc_start: 0.9017 (t0) cc_final: 0.8739 (t0) REVERT: E 73 ASP cc_start: 0.8417 (t0) cc_final: 0.8191 (t0) REVERT: G 15 GLU cc_start: 0.8694 (tp30) cc_final: 0.8458 (tp30) REVERT: G 18 ASP cc_start: 0.9071 (m-30) cc_final: 0.8834 (m-30) REVERT: G 25 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7966 (mt-10) REVERT: G 48 MET cc_start: 0.8346 (mmm) cc_final: 0.8044 (tpt) REVERT: G 93 LEU cc_start: 0.9146 (mm) cc_final: 0.8862 (mp) REVERT: I 45 LEU cc_start: 0.8777 (tp) cc_final: 0.8452 (tp) REVERT: I 55 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6586 (mm-30) REVERT: I 72 TYR cc_start: 0.8360 (p90) cc_final: 0.7911 (p90) REVERT: B 48 SER cc_start: 0.8862 (m) cc_final: 0.8535 (t) REVERT: B 60 TYR cc_start: 0.7094 (t80) cc_final: 0.6889 (t80) REVERT: B 71 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 76 ASP cc_start: 0.8696 (m-30) cc_final: 0.8403 (m-30) REVERT: D 37 ASP cc_start: 0.9158 (p0) cc_final: 0.8760 (p0) REVERT: D 47 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8258 (mm-30) REVERT: F 8 LEU cc_start: 0.8945 (mm) cc_final: 0.8728 (tp) REVERT: F 62 LEU cc_start: 0.8992 (tp) cc_final: 0.8752 (tp) REVERT: F 73 ASP cc_start: 0.8224 (t0) cc_final: 0.7898 (t0) REVERT: H 3 LYS cc_start: 0.4430 (mttt) cc_final: 0.3702 (mptt) REVERT: H 15 GLU cc_start: 0.8620 (tp30) cc_final: 0.8393 (tp30) REVERT: H 50 MET cc_start: 0.8875 (mmm) cc_final: 0.8624 (mmp) REVERT: H 85 TYR cc_start: 0.8456 (p90) cc_final: 0.7774 (p90) REVERT: H 108 LYS cc_start: 0.9308 (mttt) cc_final: 0.8925 (tppt) REVERT: H 112 ARG cc_start: 0.9345 (pmt-80) cc_final: 0.8664 (mmm160) REVERT: J 45 LEU cc_start: 0.8437 (tp) cc_final: 0.8112 (tp) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.1478 time to fit residues: 85.1960 Evaluate side-chains 265 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.079816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.060193 restraints weight = 176476.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061568 restraints weight = 103162.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.062023 restraints weight = 65878.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062147 restraints weight = 57605.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.062140 restraints weight = 55091.264| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.8074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27820 Z= 0.198 Angle : 0.672 12.013 40832 Z= 0.345 Chirality : 0.036 0.192 5130 Planarity : 0.005 0.058 2588 Dihedral : 23.719 177.554 12238 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.08 % Allowed : 0.57 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1356 helix: 0.19 (0.21), residues: 596 sheet: -0.28 (0.35), residues: 234 loop : -1.37 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 75 TYR 0.029 0.002 TYR C 196 PHE 0.023 0.002 PHE H 69 TRP 0.023 0.002 TRP H 58 HIS 0.006 0.002 HIS F 10 Details of bonding type rmsd covalent geometry : bond 0.00406 (27814) covalent geometry : angle 0.67208 (40832) hydrogen bonds : bond 0.05929 ( 992) hydrogen bonds : angle 4.17937 ( 2364) metal coordination : bond 0.00268 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8636 (m) cc_final: 0.8141 (t) REVERT: A 60 TYR cc_start: 0.7355 (t80) cc_final: 0.7092 (t80) REVERT: C 21 LYS cc_start: 0.7362 (mmmt) cc_final: 0.6764 (tmtt) REVERT: C 40 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9003 (tm-30) REVERT: C 74 PHE cc_start: 0.8541 (m-10) cc_final: 0.7865 (m-80) REVERT: E 6 ASN cc_start: 0.9121 (t0) cc_final: 0.8836 (t0) REVERT: G 15 GLU cc_start: 0.8682 (tp30) cc_final: 0.8418 (tp30) REVERT: G 18 ASP cc_start: 0.8970 (m-30) cc_final: 0.8583 (m-30) REVERT: G 20 LEU cc_start: 0.9610 (tp) cc_final: 0.9349 (tp) REVERT: G 25 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8073 (mt-10) REVERT: G 48 MET cc_start: 0.8426 (mmm) cc_final: 0.8003 (tpt) REVERT: G 56 LYS cc_start: 0.9058 (mttt) cc_final: 0.8820 (mmtp) REVERT: G 93 LEU cc_start: 0.9113 (mm) cc_final: 0.8894 (mp) REVERT: I 18 LEU cc_start: 0.9061 (mm) cc_final: 0.8747 (mm) REVERT: I 72 TYR cc_start: 0.8442 (p90) cc_final: 0.8160 (p90) REVERT: B 48 SER cc_start: 0.8725 (m) cc_final: 0.8296 (t) REVERT: B 71 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 76 ASP cc_start: 0.8738 (m-30) cc_final: 0.8468 (m-30) REVERT: D 82 LEU cc_start: 0.9174 (tp) cc_final: 0.8902 (tp) REVERT: H 3 LYS cc_start: 0.4457 (mttt) cc_final: 0.4161 (tptm) REVERT: H 15 GLU cc_start: 0.8593 (tp30) cc_final: 0.8282 (tp30) REVERT: H 48 MET cc_start: 0.8557 (ttt) cc_final: 0.8151 (tmm) REVERT: H 85 TYR cc_start: 0.8395 (p90) cc_final: 0.7781 (p90) REVERT: H 108 LYS cc_start: 0.9328 (mttt) cc_final: 0.8889 (tppt) REVERT: H 112 ARG cc_start: 0.9327 (pmt-80) cc_final: 0.8466 (mmm160) REVERT: J 45 LEU cc_start: 0.8501 (tp) cc_final: 0.7978 (tp) REVERT: J 72 TYR cc_start: 0.8365 (p90) cc_final: 0.7991 (p90) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1474 time to fit residues: 82.0340 Evaluate side-chains 256 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 154 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.079334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057991 restraints weight = 178954.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.059422 restraints weight = 101379.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060215 restraints weight = 72465.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061065 restraints weight = 60351.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061339 restraints weight = 54233.136| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27820 Z= 0.195 Angle : 0.676 10.131 40832 Z= 0.347 Chirality : 0.037 0.198 5130 Planarity : 0.005 0.055 2588 Dihedral : 23.853 175.168 12238 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1356 helix: 0.11 (0.20), residues: 596 sheet: -0.32 (0.35), residues: 232 loop : -1.56 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 75 TYR 0.024 0.002 TYR C 213 PHE 0.026 0.002 PHE D 152 TRP 0.020 0.002 TRP A 57 HIS 0.008 0.002 HIS J 60 Details of bonding type rmsd covalent geometry : bond 0.00401 (27814) covalent geometry : angle 0.67623 (40832) hydrogen bonds : bond 0.05521 ( 992) hydrogen bonds : angle 4.28043 ( 2364) metal coordination : bond 0.00201 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.75 seconds wall clock time: 99 minutes 21.35 seconds (5961.35 seconds total)