Starting phenix.real_space_refine on Sun Sep 13 19:57:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k0b_9900/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.cif" model { file = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k0b_9900/09_2026/6k0b_9900.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 5.36, 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: 2.01 Conformation dependent library (CDL) restraints added in 502.7 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: 3.40 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: 4.57 Time building geometry restraints manager: 2.82 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: 38294 2.18 - 4.35: 2283 4.35 - 6.53: 228 6.53 - 8.70: 21 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=" C3' U X 17 " pdb=" O3' U X 17 " pdb=" P C X 18 " ideal model delta sigma weight residual 119.70 125.18 -5.48 1.20e+00 6.94e-01 2.08e+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 ... (remaining 40827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 13988 33.32 - 66.63: 1298 66.63 - 99.95: 82 99.95 - 133.26: 2 133.26 - 166.57: 2 Dihedral angle restraints: 15372 sinusoidal: 11318 harmonic: 4054 Sorted by residual: dihedral pdb=" C4' G Y 37 " pdb=" C3' G Y 37 " pdb=" C2' G Y 37 " pdb=" C1' G Y 37 " ideal model delta sinusoidal sigma weight residual 36.35 -39.59 75.94 1 3.10e+00 1.04e-01 7.56e+02 dihedral pdb=" C4' G X 37 " pdb=" C3' G X 37 " pdb=" C2' G X 37 " pdb=" C1' G X 37 " ideal model delta sinusoidal sigma weight residual 36.34 -39.53 75.88 1 3.10e+00 1.04e-01 7.55e+02 dihedral pdb=" C4' A Y 27 " pdb=" C3' A Y 27 " pdb=" C2' A Y 27 " pdb=" C1' A Y 27 " ideal model delta sinusoidal sigma weight residual 36.34 -39.11 75.45 1 3.10e+00 1.04e-01 7.48e+02 ... (remaining 15369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4035 0.082 - 0.164: 251 0.164 - 0.245: 626 0.245 - 0.327: 209 0.327 - 0.409: 9 Chirality restraints: 5130 Sorted by residual: chirality pdb=" P C Y 206 " pdb=" OP1 C Y 206 " pdb=" OP2 C Y 206 " pdb=" O5' C Y 206 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" P C X 206 " pdb=" OP1 C X 206 " pdb=" OP2 C X 206 " pdb=" O5' C X 206 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" P U Y 199 " pdb=" OP1 U Y 199 " pdb=" OP2 U Y 199 " pdb=" O5' U Y 199 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.81e+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: 1.880 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.040 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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= 0.235 Angle : 1.005 10.877 40832 Z= 0.472 Chirality : 0.105 0.409 5130 Planarity : 0.006 0.086 2588 Dihedral : 18.678 166.575 12748 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/Z covalent geometry : bond 0.00365 / 0.20 (27814) covalent geometry : angle 1.00520 / 0.47 (40832) hydrogen bonds : bond 0.14339 / 8.77 ( 992) hydrogen bonds : angle 6.63199 / 4.59 ( 2364) metal coordination : bond 0.26445 / 13.04 ( 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 : 0.637 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: 0.1897 time to fit residues: 204.7662 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 : 0.435 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 10.0000 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: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** 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 = 0.4130 r_free = 0.4130 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074635 restraints weight = 172341.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.076268 restraints weight = 95455.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.077575 restraints weight = 65457.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078286 restraints weight = 51801.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.078715 restraints weight = 45333.833| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27820 Z= 0.216 Angle : 1.232 18.510 40832 Z= 0.503 Chirality : 0.102 1.727 5130 Planarity : 0.006 0.085 2588 Dihedral : 18.848 166.222 9706 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.25 % Allowed : 3.53 % Favored : 96.22 % 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: -2.16 (0.21), residues: 1356 helix: -0.97 (0.19), residues: 618 sheet: -0.78 (0.32), residues: 242 loop : -2.20 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 105 TYR 0.028 0.002 TYR D 176 PHE 0.016 0.002 PHE H 69 TRP 0.020 0.002 TRP H 58 HIS 0.004 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (27814) covalent geometry : angle 1.23213 / 0.50 (40832) hydrogen bonds : bond 0.06637 / 4.27 ( 992) hydrogen bonds : angle 4.22127 / 2.92 ( 2364) metal coordination : bond 0.00294 / 0.15 ( 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 452 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 449 time to evaluate : 0.649 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: A 65 TYR cc_start: 0.7791 (m-80) cc_final: 0.7384 (m-10) REVERT: A 76 ASP cc_start: 0.8742 (m-30) cc_final: 0.8515 (m-30) REVERT: C 7 ARG cc_start: 0.8102 (ptp-170) cc_final: 0.7756 (mtt180) REVERT: C 97 LEU cc_start: 0.8799 (pp) cc_final: 0.8375 (mt) REVERT: C 107 GLU cc_start: 0.6843 (pm20) cc_final: 0.6207 (tm-30) REVERT: C 150 LEU cc_start: 0.9374 (tp) cc_final: 0.9041 (tt) REVERT: C 167 VAL cc_start: 0.8580 (t) cc_final: 0.7927 (p) REVERT: C 213 TYR cc_start: 0.7904 (t80) cc_final: 0.7608 (t80) REVERT: E 12 LEU cc_start: 0.9116 (mt) cc_final: 0.8497 (tp) REVERT: E 82 GLU cc_start: 0.8517 (mp0) cc_final: 0.8277 (pm20) REVERT: G 12 ILE cc_start: 0.9794 (tt) cc_final: 0.8196 (tt) REVERT: G 17 ILE cc_start: 0.9376 (mm) cc_final: 0.9118 (mm) REVERT: G 25 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7756 (mt-10) REVERT: G 93 LEU cc_start: 0.8727 (mm) cc_final: 0.8336 (mt) REVERT: G 109 GLU cc_start: 0.9134 (tp30) cc_final: 0.8796 (tp30) REVERT: I 72 TYR cc_start: 0.8682 (p90) cc_final: 0.8220 (p90) REVERT: I 79 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8419 (pm20) REVERT: I 97 ILE cc_start: 0.7642 (pt) cc_final: 0.7399 (pt) REVERT: B 44 GLU cc_start: 0.8006 (tp30) cc_final: 0.7748 (tp30) REVERT: B 53 LYS cc_start: 0.8188 (tttt) cc_final: 0.7229 (ttpt) REVERT: B 65 TYR cc_start: 0.7549 (m-80) cc_final: 0.7116 (m-10) REVERT: B 71 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6863 (tm-30) REVERT: D 7 ARG cc_start: 0.8315 (ptp-170) cc_final: 0.8017 (mtm110) REVERT: D 37 ASP cc_start: 0.8964 (p0) cc_final: 0.8341 (p0) REVERT: D 74 PHE cc_start: 0.8485 (m-80) cc_final: 0.8274 (m-10) REVERT: D 96 GLU cc_start: 0.8615 (tt0) cc_final: 0.8180 (tp30) REVERT: D 97 LEU cc_start: 0.8706 (pp) cc_final: 0.8454 (mt) REVERT: D 179 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8369 (mmmt) REVERT: F 12 LEU cc_start: 0.9056 (mt) cc_final: 0.8189 (tp) REVERT: F 82 GLU cc_start: 0.8573 (mp0) cc_final: 0.8222 (pm20) REVERT: H 85 TYR cc_start: 0.8111 (p90) cc_final: 0.7600 (p90) REVERT: H 108 LYS cc_start: 0.8794 (mttt) cc_final: 0.8397 (tppt) REVERT: J 72 TYR cc_start: 0.8550 (p90) cc_final: 0.8231 (p90) outliers start: 3 outliers final: 0 residues processed: 450 average time/residue: 0.1654 time to fit residues: 114.6590 Evaluate side-chains 334 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 GLN D 66 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.091305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.071267 restraints weight = 172605.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.072771 restraints weight = 95442.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.074049 restraints weight = 65729.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.074776 restraints weight = 52210.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.075175 restraints weight = 45782.455| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 27820 Z= 0.178 Angle : 1.007 10.481 40832 Z= 0.418 Chirality : 0.078 0.967 5130 Planarity : 0.006 0.065 2588 Dihedral : 19.025 176.052 9706 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.41 % Allowed : 4.84 % Favored : 94.75 % 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: -1.27 (0.22), residues: 1356 helix: -0.08 (0.21), residues: 602 sheet: -0.47 (0.34), residues: 230 loop : -1.84 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 61 TYR 0.017 0.002 TYR G 72 PHE 0.016 0.002 PHE A 21 TRP 0.012 0.002 TRP A 57 HIS 0.003 0.001 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (27814) covalent geometry : angle 1.00697 / 0.42 (40832) hydrogen bonds : bond 0.05704 / 3.64 ( 992) hydrogen bonds : angle 3.98364 / 2.76 ( 2364) metal coordination : bond 0.00185 / 0.09 ( 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 428 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 423 time to evaluate : 0.634 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: A 5 LEU cc_start: 0.8008 (tp) cc_final: 0.7692 (tp) REVERT: A 65 TYR cc_start: 0.7834 (m-80) cc_final: 0.7358 (m-10) REVERT: A 76 ASP cc_start: 0.8877 (m-30) cc_final: 0.8570 (m-30) REVERT: A 95 ILE cc_start: 0.8753 (mm) cc_final: 0.8545 (mm) REVERT: C 40 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8875 (tm-30) REVERT: C 107 GLU cc_start: 0.6981 (pm20) cc_final: 0.6730 (tm-30) REVERT: C 213 TYR cc_start: 0.8082 (t80) cc_final: 0.7760 (t80) REVERT: E 12 LEU cc_start: 0.8995 (mt) cc_final: 0.8579 (tp) REVERT: E 21 GLU cc_start: 0.7480 (mp0) cc_final: 0.7276 (mp0) REVERT: G 12 ILE cc_start: 0.9399 (tt) cc_final: 0.8752 (tt) REVERT: G 17 ILE cc_start: 0.9460 (mm) cc_final: 0.9154 (mm) REVERT: G 25 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7818 (mt-10) REVERT: G 64 LYS cc_start: 0.9456 (mttt) cc_final: 0.9089 (mmmm) REVERT: G 93 LEU cc_start: 0.8836 (mm) cc_final: 0.8391 (mp) REVERT: I 72 TYR cc_start: 0.8636 (p90) cc_final: 0.8124 (p90) REVERT: I 79 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8430 (pm20) REVERT: B 12 LEU cc_start: 0.9402 (tp) cc_final: 0.9184 (tp) REVERT: B 34 VAL cc_start: 0.8732 (t) cc_final: 0.8513 (t) REVERT: B 44 GLU cc_start: 0.8086 (tp30) cc_final: 0.7851 (tp30) REVERT: B 53 LYS cc_start: 0.8457 (tttt) cc_final: 0.7978 (ttpt) REVERT: B 65 TYR cc_start: 0.7732 (m-80) cc_final: 0.7261 (m-10) REVERT: B 71 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 76 ASP cc_start: 0.8833 (m-30) cc_final: 0.8580 (m-30) REVERT: B 82 LEU cc_start: 0.8777 (mt) cc_final: 0.8548 (mt) REVERT: D 6 ASN cc_start: 0.7953 (t0) cc_final: 0.7628 (t0) REVERT: D 74 PHE cc_start: 0.8453 (m-80) cc_final: 0.8175 (m-10) REVERT: F 12 LEU cc_start: 0.9282 (mt) cc_final: 0.8799 (tp) REVERT: F 91 ILE cc_start: 0.9142 (tp) cc_final: 0.8883 (tt) REVERT: H 21 MET cc_start: 0.9151 (tpt) cc_final: 0.8890 (tpt) REVERT: H 108 LYS cc_start: 0.8835 (mttt) cc_final: 0.8634 (tptt) REVERT: J 61 LEU cc_start: 0.9557 (mt) cc_final: 0.9305 (mt) REVERT: J 72 TYR cc_start: 0.8478 (p90) cc_final: 0.8118 (p90) outliers start: 5 outliers final: 0 residues processed: 426 average time/residue: 0.1614 time to fit residues: 109.1906 Evaluate side-chains 318 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 GLN I 25 GLN B 36 ASN D 66 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.082946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061569 restraints weight = 175426.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062935 restraints weight = 98027.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064039 restraints weight = 69298.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064545 restraints weight = 57004.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064999 restraints weight = 51175.992| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 27820 Z= 0.284 Angle : 1.139 11.943 40832 Z= 0.478 Chirality : 0.078 1.032 5130 Planarity : 0.007 0.104 2588 Dihedral : 19.164 178.004 9706 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.33 % Allowed : 5.01 % Favored : 94.66 % 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: -1.20 (0.23), residues: 1356 helix: -0.05 (0.21), residues: 588 sheet: -0.66 (0.34), residues: 244 loop : -1.63 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 86 TYR 0.024 0.003 TYR C 143 PHE 0.022 0.003 PHE F 63 TRP 0.027 0.003 TRP H 58 HIS 0.006 0.002 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (27814) covalent geometry : angle 1.13888 / 0.48 (40832) hydrogen bonds : bond 0.08171 / 5.34 ( 992) hydrogen bonds : angle 4.34107 / 3.05 ( 2364) metal coordination : bond 0.00376 / 0.18 ( 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 377 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.590 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: A 12 LEU cc_start: 0.9677 (tp) cc_final: 0.9421 (tp) REVERT: A 34 VAL cc_start: 0.8852 (t) cc_final: 0.8246 (t) REVERT: A 65 TYR cc_start: 0.8012 (m-80) cc_final: 0.7639 (m-10) REVERT: A 71 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 21 LYS cc_start: 0.7264 (mmmt) cc_final: 0.6609 (tmtt) REVERT: C 40 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8918 (tm-30) REVERT: C 74 PHE cc_start: 0.8516 (m-80) cc_final: 0.7749 (m-80) REVERT: C 82 LEU cc_start: 0.9210 (tp) cc_final: 0.8946 (tp) REVERT: G 25 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7954 (mt-10) REVERT: G 64 LYS cc_start: 0.9430 (mttt) cc_final: 0.9163 (mmmt) REVERT: G 72 TYR cc_start: 0.8623 (m-80) cc_final: 0.8357 (m-10) REVERT: I 45 LEU cc_start: 0.8672 (tp) cc_final: 0.8451 (tp) REVERT: I 72 TYR cc_start: 0.8549 (p90) cc_final: 0.8003 (p90) REVERT: B 48 SER cc_start: 0.8908 (m) cc_final: 0.8365 (t) REVERT: B 71 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 87 GLU cc_start: 0.8299 (tp30) cc_final: 0.7481 (mm-30) REVERT: D 37 ASP cc_start: 0.8785 (p0) cc_final: 0.8571 (p0) REVERT: D 74 PHE cc_start: 0.8478 (m-80) cc_final: 0.7858 (m-80) REVERT: F 27 MET cc_start: 0.8889 (mtm) cc_final: 0.8586 (mmm) REVERT: F 57 ASP cc_start: 0.8844 (p0) cc_final: 0.8485 (p0) REVERT: F 62 LEU cc_start: 0.8977 (tp) cc_final: 0.8314 (tp) REVERT: H 85 TYR cc_start: 0.8356 (p90) cc_final: 0.7722 (p90) REVERT: H 108 LYS cc_start: 0.9054 (mttt) cc_final: 0.8627 (tppt) REVERT: J 45 LEU cc_start: 0.8424 (tp) cc_final: 0.8104 (tp) REVERT: J 72 TYR cc_start: 0.8488 (p90) cc_final: 0.8236 (p90) outliers start: 4 outliers final: 2 residues processed: 375 average time/residue: 0.1589 time to fit residues: 95.7983 Evaluate side-chains 271 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS D 66 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.085854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.064958 restraints weight = 170683.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.066379 restraints weight = 93882.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.067499 restraints weight = 65626.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.068159 restraints weight = 53238.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.068453 restraints weight = 47389.859| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27820 Z= 0.148 Angle : 0.964 11.355 40832 Z= 0.399 Chirality : 0.072 0.905 5130 Planarity : 0.005 0.087 2588 Dihedral : 18.853 175.373 9706 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.08 % Allowed : 3.45 % 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: -0.89 (0.23), residues: 1356 helix: 0.36 (0.21), residues: 590 sheet: -0.63 (0.35), residues: 228 loop : -1.58 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 75 TYR 0.020 0.002 TYR D 176 PHE 0.033 0.002 PHE A 63 TRP 0.014 0.002 TRP A 49 HIS 0.008 0.001 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (27814) covalent geometry : angle 0.96440 / 0.40 (40832) hydrogen bonds : bond 0.05018 / 3.21 ( 992) hydrogen bonds : angle 3.82836 / 2.65 ( 2364) metal coordination : bond 0.01345 / 0.67 ( 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 386 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.632 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: A 11 THR cc_start: 0.9154 (p) cc_final: 0.8715 (t) REVERT: A 71 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 84 LEU cc_start: 0.9288 (mm) cc_final: 0.8838 (tp) REVERT: C 21 LYS cc_start: 0.7376 (mmmt) cc_final: 0.6619 (tmtt) REVERT: C 40 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8918 (tm-30) REVERT: C 74 PHE cc_start: 0.8342 (m-80) cc_final: 0.7571 (m-80) REVERT: C 121 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8748 (tpp80) REVERT: E 6 ASN cc_start: 0.8983 (t0) cc_final: 0.8724 (t0) REVERT: E 73 ASP cc_start: 0.8496 (t0) cc_final: 0.8183 (t70) REVERT: G 15 GLU cc_start: 0.9085 (tp30) cc_final: 0.8737 (tp30) REVERT: G 25 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7722 (mt-10) REVERT: G 64 LYS cc_start: 0.9281 (mttt) cc_final: 0.8865 (mmmt) REVERT: G 93 LEU cc_start: 0.9060 (mm) cc_final: 0.8798 (mt) REVERT: G 109 GLU cc_start: 0.9213 (pm20) cc_final: 0.8829 (pm20) REVERT: I 72 TYR cc_start: 0.8616 (p90) cc_final: 0.8032 (p90) REVERT: I 77 SER cc_start: 0.8399 (t) cc_final: 0.7845 (t) REVERT: I 79 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8506 (pm20) REVERT: B 48 SER cc_start: 0.8814 (m) cc_final: 0.8193 (t) REVERT: B 71 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 76 ASP cc_start: 0.8822 (m-30) cc_final: 0.8490 (m-30) REVERT: B 95 ILE cc_start: 0.9024 (mm) cc_final: 0.8771 (mm) REVERT: D 74 PHE cc_start: 0.8694 (m-80) cc_final: 0.7966 (m-80) REVERT: F 57 ASP cc_start: 0.8876 (p0) cc_final: 0.8612 (p0) REVERT: F 62 LEU cc_start: 0.8973 (tp) cc_final: 0.7906 (pp) REVERT: F 73 ASP cc_start: 0.8534 (t0) cc_final: 0.8181 (t0) REVERT: H 3 LYS cc_start: 0.4553 (mttt) cc_final: 0.3701 (mttp) REVERT: H 15 GLU cc_start: 0.8968 (tp30) cc_final: 0.8751 (tp30) REVERT: H 85 TYR cc_start: 0.8502 (p90) cc_final: 0.7912 (p90) REVERT: H 108 LYS cc_start: 0.9056 (mttt) cc_final: 0.8670 (tppt) REVERT: J 11 GLU cc_start: 0.8584 (tp30) cc_final: 0.8244 (tp30) REVERT: J 15 LYS cc_start: 0.9630 (tmtt) cc_final: 0.9371 (tptp) REVERT: J 45 LEU cc_start: 0.8405 (tp) cc_final: 0.8190 (tp) REVERT: J 72 TYR cc_start: 0.8609 (p90) cc_final: 0.8189 (p90) outliers start: 1 outliers final: 0 residues processed: 386 average time/residue: 0.1584 time to fit residues: 99.6196 Evaluate side-chains 304 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.084605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.063628 restraints weight = 172863.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064999 restraints weight = 97650.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.066081 restraints weight = 69097.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.066695 restraints weight = 56501.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.066984 restraints weight = 50531.287| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27820 Z= 0.174 Angle : 0.968 12.367 40832 Z= 0.401 Chirality : 0.071 0.919 5130 Planarity : 0.006 0.083 2588 Dihedral : 18.793 176.500 9706 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.16 % Allowed : 3.37 % 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: -0.74 (0.23), residues: 1356 helix: 0.47 (0.21), residues: 604 sheet: -0.37 (0.36), residues: 224 loop : -1.62 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG C 153 TYR 0.017 0.002 TYR D 176 PHE 0.020 0.002 PHE A 63 TRP 0.009 0.002 TRP H 33 HIS 0.005 0.001 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (27814) covalent geometry : angle 0.96820 / 0.40 (40832) hydrogen bonds : bond 0.05514 / 3.55 ( 992) hydrogen bonds : angle 3.84450 / 2.67 ( 2364) metal coordination : bond 0.00223 / 0.10 ( 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 369 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.627 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: A 71 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8392 (tm-30) REVERT: C 21 LYS cc_start: 0.7367 (mmmt) cc_final: 0.6666 (tmtt) REVERT: C 40 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8916 (tm-30) REVERT: C 74 PHE cc_start: 0.8406 (m-80) cc_final: 0.7700 (m-80) REVERT: E 6 ASN cc_start: 0.8996 (t0) cc_final: 0.8668 (t0) REVERT: G 15 GLU cc_start: 0.8919 (tp30) cc_final: 0.8585 (tp30) REVERT: G 18 ASP cc_start: 0.8996 (m-30) cc_final: 0.8713 (m-30) REVERT: G 25 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7700 (mt-10) REVERT: G 64 LYS cc_start: 0.9316 (mttt) cc_final: 0.9002 (mmmt) REVERT: G 93 LEU cc_start: 0.9156 (mm) cc_final: 0.8905 (mt) REVERT: I 55 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6560 (mm-30) REVERT: I 72 TYR cc_start: 0.8524 (p90) cc_final: 0.7982 (p90) REVERT: I 79 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8524 (pm20) REVERT: B 48 SER cc_start: 0.8773 (m) cc_final: 0.8295 (t) REVERT: B 71 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 76 ASP cc_start: 0.8798 (m-30) cc_final: 0.8535 (m-30) REVERT: D 21 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6709 (tmtt) REVERT: D 74 PHE cc_start: 0.8542 (m-80) cc_final: 0.7909 (m-80) REVERT: F 6 ASN cc_start: 0.8724 (t0) cc_final: 0.8504 (t0) REVERT: F 20 VAL cc_start: 0.8140 (m) cc_final: 0.7838 (m) REVERT: F 27 MET cc_start: 0.8925 (mtm) cc_final: 0.8646 (mmm) REVERT: H 3 LYS cc_start: 0.4701 (mttt) cc_final: 0.3787 (mttp) REVERT: H 25 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8302 (mt-10) REVERT: H 85 TYR cc_start: 0.8561 (p90) cc_final: 0.7709 (p90) REVERT: H 108 LYS cc_start: 0.9049 (mttt) cc_final: 0.8679 (tppt) REVERT: J 14 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8579 (tm-30) REVERT: J 45 LEU cc_start: 0.8377 (tp) cc_final: 0.8098 (tp) REVERT: J 72 TYR cc_start: 0.8476 (p90) cc_final: 0.8145 (p90) outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.1609 time to fit residues: 96.2166 Evaluate side-chains 298 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 0.0980 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.080903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059348 restraints weight = 179190.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060769 restraints weight = 101329.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061836 restraints weight = 72604.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.062408 restraints weight = 60190.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062633 restraints weight = 54362.540| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 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 = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 27820 Z= 0.257 Angle : 1.074 12.646 40832 Z= 0.450 Chirality : 0.074 0.909 5130 Planarity : 0.006 0.106 2588 Dihedral : 18.946 176.849 9706 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.33 % Allowed : 3.12 % Favored : 96.55 % 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: -0.87 (0.23), residues: 1356 helix: 0.27 (0.21), residues: 592 sheet: -0.65 (0.35), residues: 242 loop : -1.42 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 153 TYR 0.031 0.003 TYR A 25 PHE 0.021 0.002 PHE D 152 TRP 0.015 0.002 TRP A 49 HIS 0.006 0.002 HIS G 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.26 (27814) covalent geometry : angle 1.07420 / 0.45 (40832) hydrogen bonds : bond 0.07061 / 4.51 ( 992) hydrogen bonds : angle 4.22390 / 2.96 ( 2364) metal coordination : bond 0.00538 / 0.24 ( 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 342 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 0.530 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: A 71 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 40 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9019 (tm-30) REVERT: C 47 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 74 PHE cc_start: 0.8666 (m-80) cc_final: 0.7871 (m-80) REVERT: E 6 ASN cc_start: 0.9085 (t0) cc_final: 0.8798 (t0) REVERT: E 9 ARG cc_start: 0.9331 (mmt90) cc_final: 0.9066 (mmt-90) REVERT: E 92 LEU cc_start: 0.8484 (tp) cc_final: 0.8240 (tp) REVERT: G 15 GLU cc_start: 0.8824 (tp30) cc_final: 0.8346 (tp30) REVERT: G 18 ASP cc_start: 0.9116 (m-30) cc_final: 0.8594 (m-30) REVERT: G 93 LEU cc_start: 0.9226 (mm) cc_final: 0.8893 (mp) REVERT: I 45 LEU cc_start: 0.8698 (tp) cc_final: 0.8332 (tp) REVERT: I 55 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6668 (mm-30) REVERT: I 72 TYR cc_start: 0.8645 (p90) cc_final: 0.8122 (p90) REVERT: B 11 THR cc_start: 0.9097 (p) cc_final: 0.8880 (t) REVERT: B 48 SER cc_start: 0.8661 (m) cc_final: 0.8181 (t) REVERT: B 71 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 74 PHE cc_start: 0.8832 (m-80) cc_final: 0.8190 (m-80) REVERT: D 173 GLU cc_start: 0.8072 (pm20) cc_final: 0.7812 (pm20) REVERT: D 177 GLN cc_start: 0.8638 (tt0) cc_final: 0.7648 (tt0) REVERT: F 6 ASN cc_start: 0.8919 (t0) cc_final: 0.8640 (t0) REVERT: F 27 MET cc_start: 0.8941 (mtm) cc_final: 0.8590 (mmm) REVERT: H 3 LYS cc_start: 0.4531 (mttt) cc_final: 0.4137 (tptm) REVERT: H 15 GLU cc_start: 0.8747 (tp30) cc_final: 0.8507 (tp30) REVERT: J 45 LEU cc_start: 0.8538 (tp) cc_final: 0.8210 (tp) REVERT: J 55 GLU cc_start: 0.8512 (pm20) cc_final: 0.8210 (mp0) REVERT: J 72 TYR cc_start: 0.8543 (p90) cc_final: 0.8244 (p90) outliers start: 4 outliers final: 1 residues processed: 342 average time/residue: 0.1554 time to fit residues: 87.6278 Evaluate side-chains 264 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 170 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 0.0060 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS D 66 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.082464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061449 restraints weight = 175623.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.062856 restraints weight = 97780.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063953 restraints weight = 69097.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.064460 restraints weight = 56844.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064688 restraints weight = 51199.247| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.8109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27820 Z= 0.184 Angle : 1.009 13.790 40832 Z= 0.420 Chirality : 0.072 0.876 5130 Planarity : 0.006 0.089 2588 Dihedral : 18.856 179.591 9706 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.08 % Allowed : 1.31 % Favored : 98.60 % 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: 0.43 (0.21), residues: 588 sheet: -0.63 (0.34), residues: 242 loop : -1.45 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 105 TYR 0.029 0.002 TYR C 196 PHE 0.016 0.002 PHE B 111 TRP 0.021 0.003 TRP G 58 HIS 0.006 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (27814) covalent geometry : angle 1.00855 / 0.42 (40832) hydrogen bonds : bond 0.05661 / 3.68 ( 992) hydrogen bonds : angle 4.05412 / 2.84 ( 2364) metal coordination : bond 0.00284 / 0.12 ( 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 353 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9242 (tt) cc_final: 0.8899 (mm) REVERT: A 60 TYR cc_start: 0.7626 (t80) cc_final: 0.7209 (t80) REVERT: A 71 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 73 ASP cc_start: 0.8857 (m-30) cc_final: 0.8617 (m-30) REVERT: A 84 LEU cc_start: 0.9369 (mm) cc_final: 0.8923 (tp) REVERT: C 21 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6729 (tmtt) REVERT: C 40 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8981 (tm-30) REVERT: C 47 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7993 (mm-30) REVERT: C 74 PHE cc_start: 0.8603 (m-80) cc_final: 0.7861 (m-80) REVERT: C 181 PRO cc_start: 0.9242 (Cg_endo) cc_final: 0.8974 (Cg_exo) REVERT: E 6 ASN cc_start: 0.9053 (t0) cc_final: 0.8752 (t0) REVERT: E 9 ARG cc_start: 0.9247 (mmt90) cc_final: 0.8978 (mmt-90) REVERT: E 57 ASP cc_start: 0.8889 (p0) cc_final: 0.8604 (p0) REVERT: G 15 GLU cc_start: 0.8951 (tp30) cc_final: 0.8585 (tp30) REVERT: G 18 ASP cc_start: 0.9102 (m-30) cc_final: 0.8673 (m-30) REVERT: G 56 LYS cc_start: 0.9199 (mttt) cc_final: 0.8957 (mmtp) REVERT: G 93 LEU cc_start: 0.9181 (mm) cc_final: 0.8917 (mp) REVERT: I 45 LEU cc_start: 0.8617 (tp) cc_final: 0.8305 (tp) REVERT: I 55 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6559 (mm-30) REVERT: I 72 TYR cc_start: 0.8561 (p90) cc_final: 0.8062 (p90) REVERT: B 11 THR cc_start: 0.9074 (p) cc_final: 0.8823 (t) REVERT: B 48 SER cc_start: 0.8708 (m) cc_final: 0.8215 (t) REVERT: B 71 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8231 (tm-30) REVERT: D 74 PHE cc_start: 0.8779 (m-80) cc_final: 0.8085 (m-80) REVERT: F 6 ASN cc_start: 0.8842 (t0) cc_final: 0.8577 (t0) REVERT: F 8 LEU cc_start: 0.8937 (mm) cc_final: 0.8715 (tp) REVERT: F 18 GLU cc_start: 0.8126 (tp30) cc_final: 0.7721 (tp30) REVERT: F 27 MET cc_start: 0.8949 (mtm) cc_final: 0.8571 (mmm) REVERT: H 3 LYS cc_start: 0.4461 (mttt) cc_final: 0.4138 (tptm) REVERT: H 15 GLU cc_start: 0.8801 (tp30) cc_final: 0.8515 (tp30) REVERT: J 45 LEU cc_start: 0.8620 (tp) cc_final: 0.8325 (tp) REVERT: J 55 GLU cc_start: 0.8448 (pm20) cc_final: 0.8132 (mp0) REVERT: J 72 TYR cc_start: 0.8537 (p90) cc_final: 0.8227 (p90) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.1602 time to fit residues: 91.8702 Evaluate side-chains 276 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 7.9990 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.083963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063505 restraints weight = 195112.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064877 restraints weight = 108069.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.065924 restraints weight = 77186.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066593 restraints weight = 63806.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066893 restraints weight = 57421.177| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27820 Z= 0.201 Angle : 1.027 14.020 40832 Z= 0.429 Chirality : 0.072 0.876 5130 Planarity : 0.005 0.087 2588 Dihedral : 18.859 179.837 9706 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.08 % Allowed : 0.90 % Favored : 99.01 % 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: -0.82 (0.23), residues: 1356 helix: 0.34 (0.21), residues: 588 sheet: -0.69 (0.34), residues: 236 loop : -1.39 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 112 TYR 0.025 0.002 TYR C 196 PHE 0.023 0.002 PHE D 152 TRP 0.019 0.002 TRP G 58 HIS 0.008 0.002 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (27814) covalent geometry : angle 1.02725 / 0.43 (40832) hydrogen bonds : bond 0.06043 / 3.92 ( 992) hydrogen bonds : angle 4.11086 / 2.87 ( 2364) metal coordination : bond 0.00232 / 0.10 ( 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 347 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7636 (t80) cc_final: 0.7162 (t80) REVERT: A 71 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 73 ASP cc_start: 0.8867 (m-30) cc_final: 0.8626 (m-30) REVERT: A 84 LEU cc_start: 0.9370 (mm) cc_final: 0.8912 (tp) REVERT: C 40 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9003 (tm-30) REVERT: C 74 PHE cc_start: 0.8673 (m-80) cc_final: 0.7886 (m-80) REVERT: E 6 ASN cc_start: 0.9115 (t0) cc_final: 0.8765 (t0) REVERT: E 13 ILE cc_start: 0.9697 (mm) cc_final: 0.9419 (mm) REVERT: E 57 ASP cc_start: 0.8932 (p0) cc_final: 0.8653 (p0) REVERT: E 58 ILE cc_start: 0.9302 (tp) cc_final: 0.9101 (tp) REVERT: G 15 GLU cc_start: 0.8971 (tp30) cc_final: 0.8551 (tp30) REVERT: G 18 ASP cc_start: 0.9061 (m-30) cc_final: 0.8501 (m-30) REVERT: G 56 LYS cc_start: 0.9207 (mttt) cc_final: 0.8921 (mmtp) REVERT: G 85 TYR cc_start: 0.8996 (p90) cc_final: 0.8758 (p90) REVERT: G 93 LEU cc_start: 0.9227 (mm) cc_final: 0.9016 (mp) REVERT: G 103 MET cc_start: 0.8593 (tmm) cc_final: 0.8385 (tmm) REVERT: I 55 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6532 (mm-30) REVERT: I 72 TYR cc_start: 0.8706 (p90) cc_final: 0.8231 (p90) REVERT: B 11 THR cc_start: 0.9043 (p) cc_final: 0.8837 (t) REVERT: B 48 SER cc_start: 0.8798 (m) cc_final: 0.8436 (t) REVERT: B 71 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 76 ASP cc_start: 0.8749 (m-30) cc_final: 0.8530 (m-30) REVERT: D 74 PHE cc_start: 0.8869 (m-80) cc_final: 0.8088 (m-80) REVERT: D 173 GLU cc_start: 0.7658 (pm20) cc_final: 0.7410 (pm20) REVERT: F 6 ASN cc_start: 0.8907 (t0) cc_final: 0.8675 (t0) REVERT: F 18 GLU cc_start: 0.8173 (tp30) cc_final: 0.7656 (tp30) REVERT: F 27 MET cc_start: 0.9048 (mtm) cc_final: 0.8575 (mmm) REVERT: H 3 LYS cc_start: 0.4286 (mttt) cc_final: 0.4004 (tptm) REVERT: H 15 GLU cc_start: 0.8889 (tp30) cc_final: 0.8623 (tp30) REVERT: J 15 LYS cc_start: 0.9526 (tmtt) cc_final: 0.9252 (tptp) REVERT: J 45 LEU cc_start: 0.8701 (tp) cc_final: 0.8379 (tp) REVERT: J 55 GLU cc_start: 0.8497 (pm20) cc_final: 0.8145 (mp0) REVERT: J 72 TYR cc_start: 0.8658 (p90) cc_final: 0.8270 (p90) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.1525 time to fit residues: 86.9967 Evaluate side-chains 273 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.080700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.061557 restraints weight = 196511.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062714 restraints weight = 109305.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062745 restraints weight = 79351.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063182 restraints weight = 72093.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063107 restraints weight = 67085.112| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.9193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27820 Z= 0.275 Angle : 1.144 13.828 40832 Z= 0.479 Chirality : 0.076 0.862 5130 Planarity : 0.006 0.087 2588 Dihedral : 19.106 179.978 9706 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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 : 0.00 % 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: -1.54 (0.22), residues: 1356 helix: -0.33 (0.20), residues: 606 sheet: -0.80 (0.34), residues: 230 loop : -1.85 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 153 TYR 0.027 0.003 TYR B 46 PHE 0.030 0.003 PHE D 152 TRP 0.031 0.003 TRP A 57 HIS 0.008 0.002 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (27814) covalent geometry : angle 1.14402 / 0.48 (40832) hydrogen bonds : bond 0.07762 / 4.94 ( 992) hydrogen bonds : angle 4.50348 / 3.15 ( 2364) metal coordination : bond 0.00561 / 0.23 ( 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 335 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 0.708 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 60 TYR cc_start: 0.7753 (t80) cc_final: 0.7387 (t80) REVERT: C 40 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9108 (tm-30) REVERT: E 6 ASN cc_start: 0.9264 (t0) cc_final: 0.8899 (t0) REVERT: E 13 ILE cc_start: 0.9698 (mm) cc_final: 0.9496 (mm) REVERT: E 57 ASP cc_start: 0.8978 (p0) cc_final: 0.8751 (p0) REVERT: E 58 ILE cc_start: 0.9371 (tp) cc_final: 0.9154 (tp) REVERT: E 73 ASP cc_start: 0.8962 (p0) cc_final: 0.8256 (t70) REVERT: G 15 GLU cc_start: 0.8878 (tp30) cc_final: 0.8454 (tp30) REVERT: G 18 ASP cc_start: 0.9042 (m-30) cc_final: 0.8278 (m-30) REVERT: G 56 LYS cc_start: 0.9262 (mttt) cc_final: 0.9035 (mmtp) REVERT: G 85 TYR cc_start: 0.8825 (p90) cc_final: 0.8610 (p90) REVERT: I 55 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6720 (mm-30) REVERT: I 72 TYR cc_start: 0.8698 (p90) cc_final: 0.8215 (p90) REVERT: B 16 LYS cc_start: 0.9206 (ptpt) cc_final: 0.8946 (ptpp) REVERT: B 36 ASN cc_start: 0.8229 (m-40) cc_final: 0.7919 (m-40) REVERT: B 40 LYS cc_start: 0.9310 (ptpt) cc_final: 0.8989 (ptpp) REVERT: B 48 SER cc_start: 0.8870 (m) cc_final: 0.8441 (t) REVERT: D 74 PHE cc_start: 0.8954 (m-80) cc_final: 0.8323 (m-80) REVERT: D 177 GLN cc_start: 0.8600 (tt0) cc_final: 0.7387 (tt0) REVERT: F 6 ASN cc_start: 0.9073 (t0) cc_final: 0.8771 (t0) REVERT: F 18 GLU cc_start: 0.8274 (tp30) cc_final: 0.7697 (tp30) REVERT: F 27 MET cc_start: 0.9216 (mtm) cc_final: 0.8851 (mmm) REVERT: H 3 LYS cc_start: 0.4330 (mttt) cc_final: 0.4057 (tptm) REVERT: H 15 GLU cc_start: 0.8779 (tp30) cc_final: 0.8448 (tp30) REVERT: J 45 LEU cc_start: 0.8902 (tp) cc_final: 0.8444 (tp) REVERT: J 55 GLU cc_start: 0.8557 (pm20) cc_final: 0.8118 (mm-30) REVERT: J 72 TYR cc_start: 0.8762 (p90) cc_final: 0.8237 (p90) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1613 time to fit residues: 88.0825 Evaluate side-chains 251 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 2.9990 chunk 176 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 148 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN J 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.084748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064311 restraints weight = 192196.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.065731 restraints weight = 107497.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066920 restraints weight = 76983.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067511 restraints weight = 63390.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067882 restraints weight = 57115.516| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.9070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27820 Z= 0.159 Angle : 1.031 15.366 40832 Z= 0.429 Chirality : 0.074 0.844 5130 Planarity : 0.005 0.083 2588 Dihedral : 18.858 175.989 9706 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.16 % Allowed : 0.41 % Favored : 99.43 % 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: -1.02 (0.23), residues: 1356 helix: 0.28 (0.21), residues: 570 sheet: -0.78 (0.35), residues: 240 loop : -1.58 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 75 TYR 0.038 0.002 TYR C 196 PHE 0.020 0.002 PHE D 152 TRP 0.018 0.002 TRP H 58 HIS 0.008 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (27814) covalent geometry : angle 1.03089 / 0.43 (40832) hydrogen bonds : bond 0.05209 / 3.42 ( 992) hydrogen bonds : angle 4.14672 / 2.89 ( 2364) metal coordination : bond 0.00197 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5855.57 seconds wall clock time: 101 minutes 29.85 seconds (6089.85 seconds total)