Starting phenix.real_space_refine on Sun Jun 22 03:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k0b_9900/06_2025/6k0b_9900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k0b_9900/06_2025/6k0b_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_9900/06_2025/6k0b_9900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k0b_9900/06_2025/6k0b_9900.map" model { file = "/net/cci-nas-00/data/ceres_data/6k0b_9900/06_2025/6k0b_9900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k0b_9900/06_2025/6k0b_9900.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25908 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1920 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 4, 'TRANS': 226} Chain: "E" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1030 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "U" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1762 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 36, 'rna3p_pyr': 40} Link IDs: {'rna2p': 7, 'rna3p': 75} Chain: "X" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1920 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 4, 'TRANS': 226} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1030 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "V" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1762 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 36, 'rna3p_pyr': 40} Link IDs: {'rna2p': 7, 'rna3p': 75} Chain: "Y" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4310 SG CYS G 66 184.908 52.019 87.059 1.00126.46 S ATOM 4524 SG CYS G 92 188.441 51.798 89.370 1.00152.06 S ATOM 4547 SG CYS G 95 185.654 49.143 89.613 1.00153.71 S ATOM 17263 SG CYS H 66 66.193 109.284 86.901 1.00128.02 S ATOM 17477 SG CYS H 92 62.681 109.512 89.243 1.00149.50 S ATOM 17500 SG CYS H 95 65.471 112.168 89.452 1.00152.79 S Time building chain proxies: 15.01, per 1000 atoms: 0.58 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: 6.55 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 11.17 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: 9.80 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4911 1.34 - 1.46: 9980 1.46 - 1.58: 11507 1.58 - 1.69: 1360 1.69 - 1.81: 56 Bond restraints: 27814 Sorted by residual: bond pdb=" C THR D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.332 1.358 -0.026 8.20e-03 1.49e+04 9.75e+00 bond pdb=" C THR C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.332 1.357 -0.025 8.20e-03 1.49e+04 8.93e+00 bond pdb=" C LEU I 61 " pdb=" N PRO I 62 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.00e+00 bond pdb=" C LEU J 61 " pdb=" N PRO J 62 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.69e+00 bond pdb=" N1 C X 47 " pdb=" C2 C X 47 " ideal model delta sigma weight residual 1.397 1.424 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 27809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 39866 2.18 - 4.35: 830 4.35 - 6.53: 111 6.53 - 8.70: 19 8.70 - 10.88: 6 Bond angle restraints: 40832 Sorted by residual: angle pdb=" C ILE C 226 " pdb=" N ILE C 227 " pdb=" CA ILE C 227 " ideal model delta sigma weight residual 121.97 131.32 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C ILE D 226 " pdb=" N ILE D 227 " pdb=" CA ILE D 227 " ideal model delta sigma weight residual 121.97 131.29 -9.32 1.80e+00 3.09e-01 2.68e+01 angle pdb=" C LEU D 97 " pdb=" N HIS D 98 " pdb=" CA HIS D 98 " ideal model delta sigma weight residual 122.07 128.61 -6.54 1.43e+00 4.89e-01 2.09e+01 angle pdb=" C LEU C 97 " pdb=" N HIS C 98 " pdb=" CA HIS C 98 " ideal model delta sigma weight residual 122.07 128.57 -6.50 1.43e+00 4.89e-01 2.07e+01 angle pdb=" N LEU C 51 " pdb=" CA LEU C 51 " pdb=" C LEU C 51 " ideal model delta sigma weight residual 108.60 114.15 -5.55 1.46e+00 4.69e-01 1.44e+01 ... (remaining 40827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 15926 34.82 - 69.64: 1736 69.64 - 104.46: 238 104.46 - 139.28: 0 139.28 - 174.10: 4 Dihedral angle restraints: 17904 sinusoidal: 13850 harmonic: 4054 Sorted by residual: dihedral pdb=" O4' U X 207 " pdb=" C1' U X 207 " pdb=" N1 U X 207 " pdb=" C2 U X 207 " ideal model delta sinusoidal sigma weight residual 232.00 57.90 174.10 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U Y 207 " pdb=" C1' U Y 207 " pdb=" N1 U Y 207 " pdb=" C2 U Y 207 " ideal model delta sinusoidal sigma weight residual 232.00 57.94 174.06 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4591 0.061 - 0.123: 461 0.123 - 0.184: 67 0.184 - 0.246: 9 0.246 - 0.307: 2 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE D 226 " pdb=" CA ILE D 226 " pdb=" CG1 ILE D 226 " pdb=" CG2 ILE D 226 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE B 96 " pdb=" CA ILE B 96 " pdb=" CG1 ILE B 96 " pdb=" CG2 ILE B 96 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 5127 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 64 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 63 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO B 64 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 46 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C TYR A 46 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR A 46 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 47 " -0.018 2.00e-02 2.50e+03 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 180 2.59 - 3.17: 18151 3.17 - 3.74: 45194 3.74 - 4.32: 61929 4.32 - 4.90: 87519 Nonbonded interactions: 212973 Sorted by model distance: nonbonded pdb=" OG1 THR E 41 " pdb=" OP1 A X 75 " model vdw 2.011 3.040 nonbonded pdb=" NZ LYS G 114 " pdb=" OP1 G X 125 " model vdw 2.077 3.120 nonbonded pdb=" NH2 ARG H 60 " pdb=" OP1 U Y 161 " model vdw 2.100 3.120 nonbonded pdb=" OG1 THR F 41 " pdb=" OP1 A Y 75 " model vdw 2.120 3.040 nonbonded pdb=" N2 G Y 223 " pdb=" OP2 A Y 226 " model vdw 2.153 3.120 ... (remaining 212968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'Y' selection = chain 'X' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 68.990 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.160 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.283 27820 Z= 0.223 Angle : 0.777 10.877 40832 Z= 0.423 Chirality : 0.038 0.307 5130 Planarity : 0.006 0.086 2588 Dihedral : 22.118 174.099 15280 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.66 % Allowed : 2.46 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP B 120 HIS 0.008 0.002 HIS E 10 PHE 0.035 0.004 PHE D 152 TYR 0.030 0.003 TYR B 25 ARG 0.010 0.001 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.14339 ( 992) hydrogen bonds : angle 6.63199 ( 2364) metal coordination : bond 0.26445 ( 6) covalent geometry : bond 0.00322 (27814) covalent geometry : angle 0.77654 (40832) *********************** 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 : 1.917 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: 0.8496 (tt0) cc_final: 0.8106 (tp30) REVERT: C 105 THR cc_start: 0.7576 (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: 0.7909 (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: 0.4468 time to fit residues: 474.6519 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 : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN C 180 ASN C 189 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN D 133 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN D 189 ASN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.087026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.066529 restraints weight = 175501.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.067991 restraints weight = 96464.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.068934 restraints weight = 66703.829| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27820 Z= 0.294 Angle : 0.831 10.904 40832 Z= 0.418 Chirality : 0.040 0.322 5130 Planarity : 0.007 0.076 2588 Dihedral : 23.936 177.827 12238 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.33 % Allowed : 4.35 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.22), residues: 1356 helix: -0.68 (0.20), residues: 606 sheet: -1.22 (0.31), residues: 236 loop : -1.89 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 58 HIS 0.008 0.003 HIS G 87 PHE 0.023 0.003 PHE F 61 TYR 0.038 0.003 TYR D 176 ARG 0.015 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.08185 ( 992) hydrogen bonds : angle 4.46872 ( 2364) metal coordination : bond 0.01064 ( 6) covalent geometry : bond 0.00597 (27814) covalent geometry : angle 0.83079 (40832) *********************** 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 420 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 416 time to evaluate : 1.823 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: A 5 LEU cc_start: 0.8228 (tp) cc_final: 0.7855 (tp) REVERT: A 11 THR cc_start: 0.9099 (p) cc_final: 0.8890 (p) REVERT: A 65 TYR cc_start: 0.8242 (m-80) cc_final: 0.7952 (m-10) REVERT: C 37 ASP cc_start: 0.9113 (p0) cc_final: 0.8379 (p0) REVERT: C 74 PHE cc_start: 0.8217 (m-80) cc_final: 0.7658 (m-80) REVERT: C 164 VAL cc_start: 0.9515 (t) cc_final: 0.9298 (p) REVERT: E 6 ASN cc_start: 0.9064 (m110) cc_final: 0.8836 (m110) REVERT: E 82 GLU cc_start: 0.8695 (mp0) cc_final: 0.8425 (pm20) REVERT: E 83 GLU cc_start: 0.9060 (pt0) cc_final: 0.8790 (pm20) REVERT: E 90 LYS cc_start: 0.7997 (tppt) cc_final: 0.7572 (tppt) REVERT: G 25 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7922 (mt-10) REVERT: G 109 GLU cc_start: 0.9310 (tp30) cc_final: 0.8335 (tp30) REVERT: I 66 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: I 72 TYR cc_start: 0.8900 (p90) cc_final: 0.8332 (p90) REVERT: I 97 ILE cc_start: 0.7972 (pt) cc_final: 0.7748 (pt) REVERT: I 110 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9297 (pp20) REVERT: B 11 THR cc_start: 0.9199 (p) cc_final: 0.8992 (p) REVERT: B 48 SER cc_start: 0.9057 (m) cc_final: 0.8691 (t) REVERT: B 58 LEU cc_start: 0.9339 (tp) cc_final: 0.9138 (tt) REVERT: B 65 TYR cc_start: 0.8090 (m-80) cc_final: 0.7730 (m-10) REVERT: B 76 ASP cc_start: 0.8841 (m-30) cc_final: 0.8547 (m-30) REVERT: D 37 ASP cc_start: 0.9140 (p0) cc_final: 0.8478 (p0) REVERT: F 12 LEU cc_start: 0.9327 (mt) cc_final: 0.8322 (tp) REVERT: F 13 ILE cc_start: 0.9645 (mt) cc_final: 0.9444 (mt) REVERT: F 82 GLU cc_start: 0.8629 (mp0) cc_final: 0.8427 (pm20) REVERT: H 85 TYR cc_start: 0.8116 (p90) cc_final: 0.7537 (p90) REVERT: H 108 LYS cc_start: 0.8942 (mttt) cc_final: 0.8541 (tppt) REVERT: J 60 HIS cc_start: 0.7382 (p-80) cc_final: 0.6989 (p-80) REVERT: J 72 TYR cc_start: 0.8767 (p90) cc_final: 0.8341 (p90) outliers start: 4 outliers final: 0 residues processed: 419 average time/residue: 0.3831 time to fit residues: 246.8215 Evaluate side-chains 309 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 86 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** D 126 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.086905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066575 restraints weight = 167479.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.068170 restraints weight = 90678.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.069319 restraints weight = 61865.062| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27820 Z= 0.147 Angle : 0.603 8.382 40832 Z= 0.311 Chirality : 0.034 0.208 5130 Planarity : 0.005 0.091 2588 Dihedral : 23.780 177.904 12238 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.33 % Allowed : 4.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1356 helix: -0.01 (0.21), residues: 606 sheet: -0.70 (0.32), residues: 256 loop : -1.75 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 58 HIS 0.003 0.001 HIS C 98 PHE 0.015 0.002 PHE F 61 TYR 0.023 0.002 TYR D 176 ARG 0.008 0.001 ARG G 111 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 992) hydrogen bonds : angle 4.04291 ( 2364) metal coordination : bond 0.00180 ( 6) covalent geometry : bond 0.00305 (27814) covalent geometry : angle 0.60325 (40832) *********************** 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 407 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 403 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8625 (tp) cc_final: 0.8370 (tt) REVERT: A 65 TYR cc_start: 0.8061 (m-80) cc_final: 0.7664 (m-10) REVERT: C 74 PHE cc_start: 0.8379 (m-80) cc_final: 0.7569 (m-80) REVERT: C 150 LEU cc_start: 0.9428 (tp) cc_final: 0.9148 (tt) REVERT: C 154 ASN cc_start: 0.8658 (m-40) cc_final: 0.8452 (m-40) REVERT: E 18 GLU cc_start: 0.8068 (tp30) cc_final: 0.7820 (tp30) REVERT: E 83 GLU cc_start: 0.8933 (pt0) cc_final: 0.8700 (pm20) REVERT: G 25 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7936 (mt-10) REVERT: I 72 TYR cc_start: 0.8694 (p90) cc_final: 0.8218 (p90) REVERT: B 11 THR cc_start: 0.9153 (p) cc_final: 0.8913 (p) REVERT: B 36 ASN cc_start: 0.7691 (m-40) cc_final: 0.7359 (m-40) REVERT: B 37 LEU cc_start: 0.8827 (pp) cc_final: 0.8009 (pp) REVERT: B 48 SER cc_start: 0.8882 (m) cc_final: 0.8444 (t) REVERT: B 65 TYR cc_start: 0.7867 (m-80) cc_final: 0.7429 (m-10) REVERT: B 76 ASP cc_start: 0.8800 (m-30) cc_final: 0.8529 (m-30) REVERT: D 74 PHE cc_start: 0.8281 (m-80) cc_final: 0.8017 (m-80) REVERT: F 12 LEU cc_start: 0.9094 (mt) cc_final: 0.8498 (tp) REVERT: F 57 ASP cc_start: 0.8832 (p0) cc_final: 0.8375 (p0) REVERT: F 58 ILE cc_start: 0.9292 (tp) cc_final: 0.9066 (tp) REVERT: H 17 ILE cc_start: 0.9266 (mm) cc_final: 0.8993 (mm) REVERT: H 48 MET cc_start: 0.8727 (mmm) cc_final: 0.7908 (tpp) REVERT: J 72 TYR cc_start: 0.8559 (p90) cc_final: 0.8160 (p90) outliers start: 4 outliers final: 2 residues processed: 405 average time/residue: 0.3424 time to fit residues: 221.0379 Evaluate side-chains 310 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 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 = 0.3831 r_free = 0.3831 target = 0.078348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.056851 restraints weight = 177965.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058203 restraints weight = 98324.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059236 restraints weight = 69370.057| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 27820 Z= 0.385 Angle : 0.883 11.970 40832 Z= 0.452 Chirality : 0.043 0.256 5130 Planarity : 0.008 0.138 2588 Dihedral : 24.182 178.796 12238 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 0.25 % Allowed : 5.75 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1356 helix: -0.25 (0.20), residues: 604 sheet: -0.57 (0.34), residues: 240 loop : -1.89 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 57 HIS 0.011 0.002 HIS E 10 PHE 0.039 0.003 PHE B 111 TYR 0.030 0.004 TYR C 30 ARG 0.020 0.001 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.09709 ( 992) hydrogen bonds : angle 4.77489 ( 2364) metal coordination : bond 0.00520 ( 6) covalent geometry : bond 0.00770 (27814) covalent geometry : angle 0.88262 (40832) *********************** 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 332 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8847 (m) cc_final: 0.8562 (t) REVERT: A 65 TYR cc_start: 0.8192 (m-80) cc_final: 0.7835 (m-10) REVERT: C 47 GLU cc_start: 0.8334 (tp30) cc_final: 0.8120 (tp30) REVERT: C 74 PHE cc_start: 0.8791 (m-80) cc_final: 0.7937 (m-80) REVERT: E 6 ASN cc_start: 0.9187 (t0) cc_final: 0.8869 (t0) REVERT: E 62 LEU cc_start: 0.9088 (tp) cc_final: 0.8869 (tp) REVERT: E 83 GLU cc_start: 0.9055 (pt0) cc_final: 0.8820 (pt0) REVERT: G 15 GLU cc_start: 0.8751 (tp30) cc_final: 0.8502 (tp30) REVERT: G 25 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8144 (mt-10) REVERT: G 64 LYS cc_start: 0.9427 (mttt) cc_final: 0.9217 (mmmt) REVERT: G 78 VAL cc_start: 0.9259 (t) cc_final: 0.9038 (t) REVERT: G 103 MET cc_start: 0.8663 (tmm) cc_final: 0.8377 (tmm) REVERT: I 45 LEU cc_start: 0.8724 (tp) cc_final: 0.8399 (tp) REVERT: I 72 TYR cc_start: 0.8773 (p90) cc_final: 0.8137 (p90) REVERT: B 48 SER cc_start: 0.8856 (m) cc_final: 0.8510 (t) REVERT: D 74 PHE cc_start: 0.8536 (m-80) cc_final: 0.7805 (m-80) REVERT: D 174 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7316 (p0) REVERT: F 18 GLU cc_start: 0.7975 (tp30) cc_final: 0.7074 (tp30) REVERT: F 57 ASP cc_start: 0.8704 (p0) cc_final: 0.8381 (p0) REVERT: F 62 LEU cc_start: 0.9136 (tp) cc_final: 0.8851 (tp) REVERT: H 3 LYS cc_start: 0.4741 (mttt) cc_final: 0.3990 (mttp) REVERT: H 15 GLU cc_start: 0.8631 (tp30) cc_final: 0.8394 (tp30) REVERT: H 112 ARG cc_start: 0.9493 (tmm160) cc_final: 0.9086 (ttp80) REVERT: J 45 LEU cc_start: 0.8659 (tp) cc_final: 0.8286 (tp) REVERT: J 72 TYR cc_start: 0.8722 (p90) cc_final: 0.8289 (p90) outliers start: 3 outliers final: 0 residues processed: 332 average time/residue: 0.3462 time to fit residues: 184.7831 Evaluate side-chains 230 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.078519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057053 restraints weight = 174154.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058453 restraints weight = 96195.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059460 restraints weight = 68205.118| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 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 = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27820 Z= 0.252 Angle : 0.726 10.244 40832 Z= 0.372 Chirality : 0.039 0.212 5130 Planarity : 0.006 0.092 2588 Dihedral : 24.183 178.097 12238 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1356 helix: 0.01 (0.20), residues: 604 sheet: -0.22 (0.33), residues: 252 loop : -1.95 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 49 HIS 0.005 0.002 HIS F 10 PHE 0.022 0.002 PHE H 69 TYR 0.020 0.003 TYR D 176 ARG 0.012 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.06585 ( 992) hydrogen bonds : angle 4.49695 ( 2364) metal coordination : bond 0.00318 ( 6) covalent geometry : bond 0.00514 (27814) covalent geometry : angle 0.72634 (40832) *********************** 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 313 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8780 (m) cc_final: 0.8453 (t) REVERT: A 70 CYS cc_start: 0.8596 (t) cc_final: 0.8371 (t) REVERT: C 27 PHE cc_start: 0.7870 (t80) cc_final: 0.7550 (t80) REVERT: C 37 ASP cc_start: 0.9176 (p0) cc_final: 0.8782 (p0) REVERT: E 6 ASN cc_start: 0.9065 (t0) cc_final: 0.8797 (t0) REVERT: E 18 GLU cc_start: 0.8626 (tp30) cc_final: 0.7781 (tp30) REVERT: E 31 LYS cc_start: 0.9109 (mttt) cc_final: 0.8841 (mttt) REVERT: E 70 VAL cc_start: 0.8802 (t) cc_final: 0.8554 (p) REVERT: E 83 GLU cc_start: 0.9016 (pt0) cc_final: 0.8729 (pt0) REVERT: G 15 GLU cc_start: 0.8886 (tp30) cc_final: 0.8573 (tp30) REVERT: G 25 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7833 (mt-10) REVERT: I 45 LEU cc_start: 0.8869 (tp) cc_final: 0.8636 (tp) REVERT: I 72 TYR cc_start: 0.8793 (p90) cc_final: 0.8152 (p90) REVERT: B 48 SER cc_start: 0.8897 (m) cc_final: 0.8552 (t) REVERT: D 6 ASN cc_start: 0.8714 (t0) cc_final: 0.8498 (t0) REVERT: D 74 PHE cc_start: 0.8586 (m-80) cc_final: 0.7737 (m-80) REVERT: F 6 ASN cc_start: 0.8970 (t0) cc_final: 0.8699 (t0) REVERT: F 57 ASP cc_start: 0.8795 (p0) cc_final: 0.8480 (p0) REVERT: H 3 LYS cc_start: 0.4545 (mttt) cc_final: 0.4212 (tptm) REVERT: H 15 GLU cc_start: 0.8842 (tp30) cc_final: 0.8564 (tp30) REVERT: J 45 LEU cc_start: 0.8702 (tp) cc_final: 0.8417 (tp) REVERT: J 55 GLU cc_start: 0.8651 (pm20) cc_final: 0.8170 (mp0) REVERT: J 60 HIS cc_start: 0.7722 (p-80) cc_final: 0.7494 (p-80) REVERT: J 72 TYR cc_start: 0.8823 (p90) cc_final: 0.8318 (p90) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.3502 time to fit residues: 178.0544 Evaluate side-chains 235 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 36 optimal weight: 0.1980 chunk 170 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.079818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058829 restraints weight = 175523.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.060206 restraints weight = 95680.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061279 restraints weight = 67338.103| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27820 Z= 0.170 Angle : 0.652 8.839 40832 Z= 0.336 Chirality : 0.037 0.225 5130 Planarity : 0.005 0.091 2588 Dihedral : 24.013 177.023 12238 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1356 helix: 0.25 (0.21), residues: 606 sheet: -0.10 (0.34), residues: 246 loop : -1.84 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 57 HIS 0.011 0.002 HIS I 60 PHE 0.019 0.002 PHE D 152 TYR 0.029 0.002 TYR C 196 ARG 0.010 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 992) hydrogen bonds : angle 4.31406 ( 2364) metal coordination : bond 0.00251 ( 6) covalent geometry : bond 0.00351 (27814) covalent geometry : angle 0.65191 (40832) *********************** 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 322 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8681 (m) cc_final: 0.8293 (t) REVERT: A 65 TYR cc_start: 0.7679 (m-10) cc_final: 0.7161 (m-10) REVERT: A 76 ASP cc_start: 0.8678 (m-30) cc_final: 0.8446 (m-30) REVERT: C 37 ASP cc_start: 0.9067 (p0) cc_final: 0.8620 (p0) REVERT: C 74 PHE cc_start: 0.8638 (m-10) cc_final: 0.8215 (m-80) REVERT: E 6 ASN cc_start: 0.8969 (t0) cc_final: 0.8700 (t0) REVERT: E 18 GLU cc_start: 0.8292 (tp30) cc_final: 0.7585 (tp30) REVERT: E 31 LYS cc_start: 0.8971 (mttt) cc_final: 0.8688 (mttt) REVERT: G 15 GLU cc_start: 0.8692 (tp30) cc_final: 0.8442 (tp30) REVERT: G 25 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 103 MET cc_start: 0.8509 (tmm) cc_final: 0.8185 (tmm) REVERT: G 112 ARG cc_start: 0.9283 (pmt-80) cc_final: 0.8482 (mmp-170) REVERT: I 45 LEU cc_start: 0.8744 (tp) cc_final: 0.8479 (tp) REVERT: I 55 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6565 (mm-30) REVERT: I 72 TYR cc_start: 0.8616 (p90) cc_final: 0.8023 (p90) REVERT: B 103 THR cc_start: 0.8647 (m) cc_final: 0.8381 (p) REVERT: D 4 ASP cc_start: 0.7866 (t70) cc_final: 0.6807 (t70) REVERT: D 6 ASN cc_start: 0.8403 (t0) cc_final: 0.7509 (m-40) REVERT: D 37 ASP cc_start: 0.9057 (p0) cc_final: 0.8855 (p0) REVERT: F 6 ASN cc_start: 0.8876 (t0) cc_final: 0.8553 (t0) REVERT: F 75 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8317 (mtm180) REVERT: H 3 LYS cc_start: 0.4580 (mttt) cc_final: 0.4295 (tptm) REVERT: H 15 GLU cc_start: 0.8754 (tp30) cc_final: 0.8465 (tp30) REVERT: J 55 GLU cc_start: 0.8469 (pm20) cc_final: 0.8106 (mp0) REVERT: J 72 TYR cc_start: 0.8706 (p90) cc_final: 0.8281 (p90) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3897 time to fit residues: 205.8075 Evaluate side-chains 253 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 190 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.079922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059010 restraints weight = 195394.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.060414 restraints weight = 107516.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061605 restraints weight = 76614.809| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.8246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27820 Z= 0.228 Angle : 0.711 8.487 40832 Z= 0.368 Chirality : 0.039 0.217 5130 Planarity : 0.006 0.080 2588 Dihedral : 24.097 177.100 12238 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1356 helix: 0.13 (0.20), residues: 604 sheet: -0.26 (0.35), residues: 238 loop : -1.74 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 58 HIS 0.005 0.002 HIS I 60 PHE 0.031 0.003 PHE D 151 TYR 0.021 0.003 TYR B 46 ARG 0.013 0.001 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.06649 ( 992) hydrogen bonds : angle 4.39747 ( 2364) metal coordination : bond 0.00327 ( 6) covalent geometry : bond 0.00462 (27814) covalent geometry : angle 0.71123 (40832) *********************** 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 307 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.9171 (ptpt) cc_final: 0.8941 (ptpp) REVERT: A 48 SER cc_start: 0.8910 (m) cc_final: 0.8556 (t) REVERT: A 60 TYR cc_start: 0.7715 (t80) cc_final: 0.7441 (t80) REVERT: A 76 ASP cc_start: 0.8800 (m-30) cc_final: 0.8526 (m-30) REVERT: A 103 THR cc_start: 0.8945 (m) cc_final: 0.8683 (p) REVERT: C 47 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8158 (mp0) REVERT: C 82 LEU cc_start: 0.9152 (tp) cc_final: 0.8893 (tp) REVERT: E 6 ASN cc_start: 0.9149 (t0) cc_final: 0.8876 (t0) REVERT: E 9 ARG cc_start: 0.9176 (mmt90) cc_final: 0.8852 (mmt-90) REVERT: E 18 GLU cc_start: 0.8353 (tp30) cc_final: 0.7752 (tp30) REVERT: G 15 GLU cc_start: 0.8894 (tp30) cc_final: 0.8564 (tp30) REVERT: G 18 ASP cc_start: 0.9139 (m-30) cc_final: 0.8875 (m-30) REVERT: G 25 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8219 (mt-10) REVERT: I 55 GLU cc_start: 0.7795 (mm-30) cc_final: 0.6728 (mm-30) REVERT: I 72 TYR cc_start: 0.8728 (p90) cc_final: 0.8181 (p90) REVERT: I 80 ASP cc_start: 0.9275 (t0) cc_final: 0.9050 (p0) REVERT: I 81 LEU cc_start: 0.9593 (mt) cc_final: 0.9290 (mt) REVERT: B 103 THR cc_start: 0.8987 (m) cc_final: 0.8675 (p) REVERT: D 6 ASN cc_start: 0.8480 (t0) cc_final: 0.8239 (t0) REVERT: D 13 ASP cc_start: 0.9001 (t70) cc_final: 0.8712 (p0) REVERT: F 6 ASN cc_start: 0.9109 (t0) cc_final: 0.8759 (t0) REVERT: F 7 ILE cc_start: 0.9210 (mm) cc_final: 0.8966 (tp) REVERT: H 3 LYS cc_start: 0.4365 (mttt) cc_final: 0.4146 (tptm) REVERT: H 15 GLU cc_start: 0.8890 (tp30) cc_final: 0.8559 (tp30) REVERT: J 55 GLU cc_start: 0.8539 (pm20) cc_final: 0.8181 (mp0) REVERT: J 72 TYR cc_start: 0.8844 (p90) cc_final: 0.8300 (p90) REVERT: J 81 LEU cc_start: 0.9713 (mt) cc_final: 0.9381 (mt) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4421 time to fit residues: 224.9386 Evaluate side-chains 245 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.990 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 169 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.079745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060440 restraints weight = 195678.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061519 restraints weight = 117109.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062061 restraints weight = 77781.839| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.8630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27820 Z= 0.220 Angle : 0.703 10.426 40832 Z= 0.362 Chirality : 0.039 0.221 5130 Planarity : 0.006 0.108 2588 Dihedral : 24.134 173.901 12238 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1356 helix: 0.11 (0.20), residues: 592 sheet: -0.11 (0.38), residues: 202 loop : -1.66 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 57 HIS 0.005 0.002 HIS F 10 PHE 0.022 0.002 PHE H 69 TYR 0.041 0.003 TYR C 196 ARG 0.011 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.06073 ( 992) hydrogen bonds : angle 4.39858 ( 2364) metal coordination : bond 0.00320 ( 6) covalent geometry : bond 0.00446 (27814) covalent geometry : angle 0.70264 (40832) *********************** 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 304 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8924 (ptpp) REVERT: A 48 SER cc_start: 0.8933 (m) cc_final: 0.8480 (t) REVERT: A 60 TYR cc_start: 0.7682 (t80) cc_final: 0.7308 (t80) REVERT: A 103 THR cc_start: 0.9120 (m) cc_final: 0.8833 (p) REVERT: C 37 ASP cc_start: 0.9401 (p0) cc_final: 0.9060 (p0) REVERT: C 47 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8281 (mp0) REVERT: C 82 LEU cc_start: 0.9143 (tp) cc_final: 0.8897 (tp) REVERT: E 6 ASN cc_start: 0.9121 (t0) cc_final: 0.8857 (t0) REVERT: G 15 GLU cc_start: 0.8850 (tp30) cc_final: 0.8520 (tp30) REVERT: G 25 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 109 GLU cc_start: 0.9386 (mp0) cc_final: 0.9153 (mp0) REVERT: G 112 ARG cc_start: 0.9500 (pmt-80) cc_final: 0.8173 (mmm160) REVERT: I 55 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6485 (mm-30) REVERT: I 72 TYR cc_start: 0.8645 (p90) cc_final: 0.8151 (p90) REVERT: I 81 LEU cc_start: 0.9734 (mt) cc_final: 0.9361 (mt) REVERT: B 103 THR cc_start: 0.9099 (m) cc_final: 0.8812 (p) REVERT: D 176 TYR cc_start: 0.8186 (m-10) cc_final: 0.7906 (m-10) REVERT: F 6 ASN cc_start: 0.9075 (t0) cc_final: 0.8757 (t0) REVERT: H 15 GLU cc_start: 0.8814 (tp30) cc_final: 0.8458 (tp30) REVERT: J 55 GLU cc_start: 0.8379 (pm20) cc_final: 0.8040 (mp0) REVERT: J 72 TYR cc_start: 0.8805 (p90) cc_final: 0.8278 (p90) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.4875 time to fit residues: 251.7070 Evaluate side-chains 250 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 0.0060 chunk 169 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.078915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057731 restraints weight = 176537.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059164 restraints weight = 99569.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060225 restraints weight = 70441.704| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 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 = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.8655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27820 Z= 0.152 Angle : 0.647 11.730 40832 Z= 0.334 Chirality : 0.037 0.207 5130 Planarity : 0.005 0.094 2588 Dihedral : 23.969 172.862 12238 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1356 helix: 0.25 (0.21), residues: 602 sheet: -0.18 (0.34), residues: 240 loop : -1.76 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 57 HIS 0.007 0.001 HIS F 10 PHE 0.022 0.002 PHE F 63 TYR 0.019 0.002 TYR G 72 ARG 0.004 0.001 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 992) hydrogen bonds : angle 4.13317 ( 2364) metal coordination : bond 0.00414 ( 6) covalent geometry : bond 0.00311 (27814) covalent geometry : angle 0.64706 (40832) *********************** 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 323 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.756 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: A 36 ASN cc_start: 0.8490 (m-40) cc_final: 0.8272 (m-40) REVERT: A 48 SER cc_start: 0.8712 (m) cc_final: 0.8424 (t) REVERT: A 60 TYR cc_start: 0.7563 (t80) cc_final: 0.7258 (t80) REVERT: A 71 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 103 THR cc_start: 0.8942 (m) cc_final: 0.8617 (p) REVERT: C 6 ASN cc_start: 0.8720 (t0) cc_final: 0.8280 (t0) REVERT: C 37 ASP cc_start: 0.9277 (p0) cc_final: 0.8897 (p0) REVERT: C 82 LEU cc_start: 0.9048 (tp) cc_final: 0.8841 (tp) REVERT: E 6 ASN cc_start: 0.8965 (t0) cc_final: 0.8729 (t0) REVERT: G 15 GLU cc_start: 0.8886 (tp30) cc_final: 0.8583 (tp30) REVERT: G 18 ASP cc_start: 0.9163 (m-30) cc_final: 0.8785 (m-30) REVERT: G 48 MET cc_start: 0.8869 (ttt) cc_final: 0.8468 (tmm) REVERT: G 103 MET cc_start: 0.8668 (tmm) cc_final: 0.8196 (tmm) REVERT: G 111 ARG cc_start: 0.8257 (tpt90) cc_final: 0.7173 (tpm170) REVERT: G 115 LEU cc_start: 0.9116 (mm) cc_final: 0.8623 (mm) REVERT: I 72 TYR cc_start: 0.8627 (p90) cc_final: 0.8164 (p90) REVERT: I 80 ASP cc_start: 0.8420 (p0) cc_final: 0.8218 (p0) REVERT: B 60 TYR cc_start: 0.7465 (t80) cc_final: 0.7259 (t80) REVERT: B 103 THR cc_start: 0.9093 (m) cc_final: 0.8802 (p) REVERT: D 21 LYS cc_start: 0.7521 (mmmt) cc_final: 0.6769 (tttm) REVERT: D 176 TYR cc_start: 0.8023 (m-10) cc_final: 0.7697 (m-10) REVERT: D 190 THR cc_start: 0.8810 (m) cc_final: 0.8596 (m) REVERT: F 6 ASN cc_start: 0.8993 (t0) cc_final: 0.8741 (t0) REVERT: F 18 GLU cc_start: 0.8282 (tp30) cc_final: 0.7814 (tp30) REVERT: H 15 GLU cc_start: 0.8853 (tp30) cc_final: 0.8597 (tp30) REVERT: J 55 GLU cc_start: 0.8348 (pm20) cc_final: 0.8015 (mp0) REVERT: J 72 TYR cc_start: 0.8711 (p90) cc_final: 0.8219 (p90) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.3390 time to fit residues: 179.5580 Evaluate side-chains 254 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** 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 = 0.3799 r_free = 0.3799 target = 0.076681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056426 restraints weight = 175350.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057651 restraints weight = 103128.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.058134 restraints weight = 76017.478| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.9061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27820 Z= 0.234 Angle : 0.723 10.844 40832 Z= 0.374 Chirality : 0.039 0.231 5130 Planarity : 0.006 0.094 2588 Dihedral : 24.078 171.649 12238 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1356 helix: -0.03 (0.21), residues: 582 sheet: -0.29 (0.35), residues: 234 loop : -1.78 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 58 HIS 0.013 0.002 HIS I 60 PHE 0.022 0.002 PHE H 69 TYR 0.023 0.002 TYR D 196 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.06646 ( 992) hydrogen bonds : angle 4.48619 ( 2364) metal coordination : bond 0.00354 ( 6) covalent geometry : bond 0.00475 (27814) covalent geometry : angle 0.72331 (40832) ********************** 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 298 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8817 (m) cc_final: 0.8528 (t) REVERT: A 60 TYR cc_start: 0.7588 (t80) cc_final: 0.7161 (t80) REVERT: A 103 THR cc_start: 0.9063 (m) cc_final: 0.8713 (p) REVERT: C 82 LEU cc_start: 0.9231 (tp) cc_final: 0.9008 (tp) REVERT: C 84 GLU cc_start: 0.7187 (tt0) cc_final: 0.6711 (tm-30) REVERT: E 6 ASN cc_start: 0.9109 (t0) cc_final: 0.8819 (t0) REVERT: E 18 GLU cc_start: 0.8173 (tp30) cc_final: 0.7549 (tp30) REVERT: G 15 GLU cc_start: 0.8862 (tp30) cc_final: 0.8518 (tp30) REVERT: G 18 ASP cc_start: 0.9116 (m-30) cc_final: 0.8787 (m-30) REVERT: G 25 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8503 (mt-10) REVERT: G 56 LYS cc_start: 0.9303 (mttt) cc_final: 0.8958 (mmmm) REVERT: G 103 MET cc_start: 0.8610 (tmm) cc_final: 0.8210 (tmm) REVERT: G 111 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7795 (tpp-160) REVERT: G 115 LEU cc_start: 0.9141 (mm) cc_final: 0.8861 (mm) REVERT: I 72 TYR cc_start: 0.8500 (p90) cc_final: 0.8136 (p90) REVERT: B 103 THR cc_start: 0.9195 (m) cc_final: 0.8894 (p) REVERT: D 4 ASP cc_start: 0.7916 (t70) cc_final: 0.6512 (t70) REVERT: D 6 ASN cc_start: 0.8607 (t0) cc_final: 0.7683 (m-40) REVERT: D 170 THR cc_start: 0.9244 (p) cc_final: 0.9018 (p) REVERT: D 176 TYR cc_start: 0.8199 (m-10) cc_final: 0.7871 (m-10) REVERT: F 6 ASN cc_start: 0.9128 (t0) cc_final: 0.8786 (t0) REVERT: H 15 GLU cc_start: 0.8795 (tp30) cc_final: 0.8438 (tp30) REVERT: H 48 MET cc_start: 0.8827 (mmm) cc_final: 0.8445 (mmm) REVERT: J 11 GLU cc_start: 0.8499 (tp30) cc_final: 0.8224 (tp30) REVERT: J 72 TYR cc_start: 0.8630 (p90) cc_final: 0.8137 (p90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3399 time to fit residues: 168.0656 Evaluate side-chains 240 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 61 optimal weight: 0.9980 chunk 140 optimal weight: 0.0270 chunk 83 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.079723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060304 restraints weight = 174377.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061452 restraints weight = 104895.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062049 restraints weight = 68388.053| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.8946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27820 Z= 0.131 Angle : 0.649 13.287 40832 Z= 0.334 Chirality : 0.037 0.272 5130 Planarity : 0.005 0.091 2588 Dihedral : 23.893 171.365 12238 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1356 helix: 0.22 (0.21), residues: 596 sheet: -0.21 (0.34), residues: 254 loop : -1.77 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 58 HIS 0.010 0.002 HIS E 10 PHE 0.021 0.002 PHE A 111 TYR 0.020 0.002 TYR D 213 ARG 0.012 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 992) hydrogen bonds : angle 4.19694 ( 2364) metal coordination : bond 0.00102 ( 6) covalent geometry : bond 0.00274 (27814) covalent geometry : angle 0.64910 (40832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10728.16 seconds wall clock time: 190 minutes 58.55 seconds (11458.55 seconds total)