Starting phenix.real_space_refine on Mon Sep 30 14:10:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_9900.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_9900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_9900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_9900.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/09_2024/6k0b_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-5461/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: 14.63, per 1000 atoms: 0.56 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: 6.61 Conformation dependent library (CDL) restraints added in 1.8 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: 9.03 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: 8.06 Time building geometry restraints manager: 7.50 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 62.190 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.870 ------------------------------------------------------------------------------- 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 : 0.003 0.040 27814 Z= 0.200 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 723 time to evaluate : 1.628 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: 0.4429 time to fit residues: 468.2158 Evaluate side-chains 362 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 27814 Z= 0.369 Angle : 0.830 10.909 40832 Z= 0.418 Chirality : 0.040 0.322 5130 Planarity : 0.007 0.076 2588 Dihedral : 23.936 177.831 12238 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 21.87 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: -1.94 (0.22), residues: 1356 helix: -0.69 (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 *********************** 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 fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 1.874 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: 0.8190 (tp) cc_final: 0.7809 (tp) REVERT: A 65 TYR cc_start: 0.8100 (m-80) cc_final: 0.7840 (m-10) REVERT: C 37 ASP cc_start: 0.9000 (p0) cc_final: 0.8211 (p0) REVERT: C 74 PHE cc_start: 0.8122 (m-80) cc_final: 0.7615 (m-80) REVERT: C 164 VAL cc_start: 0.9498 (t) cc_final: 0.9280 (p) REVERT: E 6 ASN cc_start: 0.9083 (m110) cc_final: 0.8814 (m110) REVERT: E 82 GLU cc_start: 0.8642 (mp0) cc_final: 0.8385 (pm20) REVERT: E 83 GLU cc_start: 0.9055 (pt0) cc_final: 0.8782 (pm20) REVERT: E 90 LYS cc_start: 0.7984 (tppt) cc_final: 0.7600 (tppt) REVERT: G 25 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7886 (mt-10) REVERT: G 109 GLU cc_start: 0.9120 (tp30) cc_final: 0.8084 (tp30) REVERT: I 66 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: I 72 TYR cc_start: 0.8668 (p90) cc_final: 0.8237 (p90) REVERT: I 110 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9217 (pp20) REVERT: B 48 SER cc_start: 0.9146 (m) cc_final: 0.8776 (t) REVERT: B 65 TYR cc_start: 0.7943 (m-80) cc_final: 0.7614 (m-10) REVERT: B 76 ASP cc_start: 0.8892 (m-30) cc_final: 0.8601 (m-30) REVERT: D 37 ASP cc_start: 0.8976 (p0) cc_final: 0.8278 (p0) REVERT: F 12 LEU cc_start: 0.9350 (mt) cc_final: 0.8348 (tp) REVERT: F 82 GLU cc_start: 0.8606 (mp0) cc_final: 0.8401 (pm20) REVERT: F 83 GLU cc_start: 0.9079 (pt0) cc_final: 0.8862 (pm20) REVERT: H 12 ILE cc_start: 0.9490 (mm) cc_final: 0.9278 (tt) REVERT: H 85 TYR cc_start: 0.8096 (p90) cc_final: 0.7449 (p90) REVERT: H 108 LYS cc_start: 0.8912 (mttt) cc_final: 0.8498 (tppt) REVERT: J 60 HIS cc_start: 0.7280 (p-80) cc_final: 0.6876 (p-80) REVERT: J 72 TYR cc_start: 0.8533 (p90) cc_final: 0.8229 (p90) outliers start: 4 outliers final: 0 residues processed: 419 average time/residue: 0.3858 time to fit residues: 247.5212 Evaluate side-chains 305 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27814 Z= 0.196 Angle : 0.608 8.373 40832 Z= 0.314 Chirality : 0.034 0.207 5130 Planarity : 0.005 0.090 2588 Dihedral : 23.790 178.075 12238 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.41 % Allowed : 4.76 % Favored : 94.83 % 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: -1.17 (0.23), residues: 1356 helix: 0.05 (0.21), residues: 606 sheet: -0.73 (0.33), residues: 246 loop : -1.71 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 58 HIS 0.004 0.001 HIS C 98 PHE 0.019 0.002 PHE B 111 TYR 0.026 0.002 TYR D 176 ARG 0.008 0.001 ARG G 111 *********************** 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 402 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 397 time to evaluate : 1.780 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: A 29 LEU cc_start: 0.8637 (tp) cc_final: 0.8333 (tt) REVERT: A 65 TYR cc_start: 0.8019 (m-80) cc_final: 0.7635 (m-10) REVERT: C 74 PHE cc_start: 0.8356 (m-80) cc_final: 0.7553 (m-80) REVERT: C 228 LYS cc_start: 0.8934 (mttt) cc_final: 0.8672 (tmtt) REVERT: E 83 GLU cc_start: 0.8971 (pt0) cc_final: 0.8720 (pm20) REVERT: G 21 MET cc_start: 0.9233 (tpt) cc_final: 0.9020 (tpt) REVERT: G 25 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7880 (mt-10) REVERT: I 72 TYR cc_start: 0.8527 (p90) cc_final: 0.8154 (p90) REVERT: B 36 ASN cc_start: 0.7640 (m-40) cc_final: 0.7300 (m-40) REVERT: B 48 SER cc_start: 0.8985 (m) cc_final: 0.8535 (t) REVERT: B 76 ASP cc_start: 0.8883 (m-30) cc_final: 0.8607 (m-30) REVERT: B 95 ILE cc_start: 0.8992 (mm) cc_final: 0.8785 (mm) REVERT: D 74 PHE cc_start: 0.8335 (m-80) cc_final: 0.8089 (m-80) REVERT: F 12 LEU cc_start: 0.9141 (mt) cc_final: 0.8553 (tp) REVERT: H 17 ILE cc_start: 0.9359 (mm) cc_final: 0.9062 (mm) REVERT: H 48 MET cc_start: 0.8844 (mmm) cc_final: 0.7956 (tpp) REVERT: H 85 TYR cc_start: 0.8329 (p90) cc_final: 0.7799 (p90) REVERT: J 72 TYR cc_start: 0.8371 (p90) cc_final: 0.8066 (p90) outliers start: 5 outliers final: 2 residues processed: 400 average time/residue: 0.3450 time to fit residues: 220.0760 Evaluate side-chains 304 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 0.0020 chunk 86 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 27814 Z= 0.367 Angle : 0.799 10.454 40832 Z= 0.406 Chirality : 0.040 0.290 5130 Planarity : 0.007 0.104 2588 Dihedral : 24.054 178.439 12238 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 0.25 % Allowed : 5.83 % Favored : 93.92 % 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: -1.24 (0.22), residues: 1356 helix: -0.01 (0.20), residues: 606 sheet: -0.52 (0.34), residues: 224 loop : -1.85 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 57 HIS 0.005 0.002 HIS F 10 PHE 0.034 0.003 PHE B 111 TYR 0.023 0.003 TYR D 176 ARG 0.010 0.001 ARG G 105 *********************** 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 344 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 341 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.9022 (m) cc_final: 0.8644 (t) REVERT: A 65 TYR cc_start: 0.8147 (m-80) cc_final: 0.7610 (m-10) REVERT: C 27 PHE cc_start: 0.7784 (t80) cc_final: 0.7553 (t80) REVERT: C 74 PHE cc_start: 0.8730 (m-80) cc_final: 0.7847 (m-80) REVERT: C 228 LYS cc_start: 0.9107 (mttt) cc_final: 0.8872 (mptt) REVERT: E 6 ASN cc_start: 0.9066 (m110) cc_final: 0.8717 (t0) REVERT: E 18 GLU cc_start: 0.8326 (tp30) cc_final: 0.7814 (tp30) REVERT: E 83 GLU cc_start: 0.9112 (pt0) cc_final: 0.8900 (pt0) REVERT: G 15 GLU cc_start: 0.8921 (tp30) cc_final: 0.8660 (tp30) REVERT: G 25 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 64 LYS cc_start: 0.9455 (mttt) cc_final: 0.9244 (mmmt) REVERT: G 78 VAL cc_start: 0.9221 (t) cc_final: 0.8990 (t) REVERT: I 45 LEU cc_start: 0.8474 (tp) cc_final: 0.8220 (tp) REVERT: I 72 TYR cc_start: 0.8500 (p90) cc_final: 0.8058 (p90) REVERT: B 48 SER cc_start: 0.8919 (m) cc_final: 0.8471 (t) REVERT: D 47 GLU cc_start: 0.8195 (tp30) cc_final: 0.7828 (tp30) REVERT: D 74 PHE cc_start: 0.8457 (m-80) cc_final: 0.7683 (m-80) REVERT: D 174 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7499 (p0) REVERT: H 3 LYS cc_start: 0.5002 (mttt) cc_final: 0.4141 (mttp) REVERT: H 15 GLU cc_start: 0.8929 (tp30) cc_final: 0.8671 (tp30) REVERT: H 85 TYR cc_start: 0.8351 (p90) cc_final: 0.7739 (p90) REVERT: H 112 ARG cc_start: 0.9388 (tmm160) cc_final: 0.9043 (ttp80) REVERT: J 11 GLU cc_start: 0.8580 (tp30) cc_final: 0.8099 (tp30) REVERT: J 45 LEU cc_start: 0.8449 (tp) cc_final: 0.8169 (tp) REVERT: J 72 TYR cc_start: 0.8472 (p90) cc_final: 0.8128 (p90) outliers start: 3 outliers final: 1 residues processed: 343 average time/residue: 0.3674 time to fit residues: 200.7185 Evaluate side-chains 249 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 48 optimal weight: 0.0370 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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** I 60 HIS ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27814 Z= 0.218 Angle : 0.641 8.283 40832 Z= 0.331 Chirality : 0.036 0.205 5130 Planarity : 0.006 0.091 2588 Dihedral : 23.923 178.298 12238 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.96 (0.23), residues: 1356 helix: 0.28 (0.21), residues: 606 sheet: -0.45 (0.32), residues: 254 loop : -1.82 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 49 HIS 0.004 0.001 HIS E 10 PHE 0.016 0.002 PHE H 69 TYR 0.018 0.002 TYR C 176 ARG 0.013 0.001 ARG H 105 *********************** 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 338 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8273 (m-40) cc_final: 0.8011 (m-40) REVERT: A 48 SER cc_start: 0.8863 (m) cc_final: 0.8463 (t) REVERT: A 65 TYR cc_start: 0.7910 (m-80) cc_final: 0.7705 (m-10) REVERT: C 37 ASP cc_start: 0.8949 (p0) cc_final: 0.8700 (p0) REVERT: C 74 PHE cc_start: 0.8641 (m-80) cc_final: 0.7827 (m-80) REVERT: C 228 LYS cc_start: 0.8968 (mttt) cc_final: 0.8727 (mptt) REVERT: E 6 ASN cc_start: 0.8983 (m110) cc_final: 0.8673 (t0) REVERT: E 83 GLU cc_start: 0.9038 (pt0) cc_final: 0.8753 (pt0) REVERT: G 15 GLU cc_start: 0.8917 (tp30) cc_final: 0.8683 (tp30) REVERT: G 18 ASP cc_start: 0.9037 (m-30) cc_final: 0.8782 (m-30) REVERT: G 25 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7922 (mt-10) REVERT: G 78 VAL cc_start: 0.9201 (t) cc_final: 0.8996 (t) REVERT: G 85 TYR cc_start: 0.8575 (p90) cc_final: 0.8364 (p90) REVERT: B 48 SER cc_start: 0.8829 (m) cc_final: 0.8405 (t) REVERT: D 37 ASP cc_start: 0.8904 (p0) cc_final: 0.8696 (p0) REVERT: D 74 PHE cc_start: 0.8537 (m-80) cc_final: 0.7756 (m-80) REVERT: F 6 ASN cc_start: 0.8752 (t0) cc_final: 0.8508 (t0) REVERT: H 3 LYS cc_start: 0.4962 (mttt) cc_final: 0.4679 (tptm) REVERT: H 15 GLU cc_start: 0.9000 (tp30) cc_final: 0.8739 (tp30) REVERT: H 85 TYR cc_start: 0.8511 (p90) cc_final: 0.8167 (p90) REVERT: J 45 LEU cc_start: 0.8393 (tp) cc_final: 0.8063 (tp) REVERT: J 55 GLU cc_start: 0.8473 (pm20) cc_final: 0.8096 (mp0) REVERT: J 72 TYR cc_start: 0.8424 (p90) cc_final: 0.8040 (p90) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.3400 time to fit residues: 186.7744 Evaluate side-chains 256 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ** 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 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27814 Z= 0.190 Angle : 0.614 8.445 40832 Z= 0.317 Chirality : 0.035 0.215 5130 Planarity : 0.005 0.097 2588 Dihedral : 23.781 178.515 12238 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.82 (0.23), residues: 1356 helix: 0.42 (0.21), residues: 606 sheet: -0.49 (0.32), residues: 258 loop : -1.72 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 58 HIS 0.004 0.001 HIS F 10 PHE 0.016 0.002 PHE B 111 TYR 0.030 0.002 TYR C 196 ARG 0.009 0.001 ARG D 7 *********************** 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 342 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8295 (m-40) cc_final: 0.8005 (m-40) REVERT: A 48 SER cc_start: 0.8943 (m) cc_final: 0.8558 (t) REVERT: A 103 THR cc_start: 0.9055 (m) cc_final: 0.8759 (p) REVERT: C 74 PHE cc_start: 0.8625 (m-80) cc_final: 0.7811 (m-80) REVERT: C 228 LYS cc_start: 0.8890 (mttt) cc_final: 0.8655 (mptt) REVERT: E 6 ASN cc_start: 0.8790 (m110) cc_final: 0.8499 (t0) REVERT: G 15 GLU cc_start: 0.8903 (tp30) cc_final: 0.8646 (tp30) REVERT: G 18 ASP cc_start: 0.9088 (m-30) cc_final: 0.8696 (m-30) REVERT: G 25 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8066 (mt-10) REVERT: G 48 MET cc_start: 0.8475 (mmm) cc_final: 0.8232 (mmm) REVERT: G 106 GLU cc_start: 0.8381 (mp0) cc_final: 0.7993 (mp0) REVERT: I 45 LEU cc_start: 0.8698 (tp) cc_final: 0.8400 (tp) REVERT: I 72 TYR cc_start: 0.8493 (p90) cc_final: 0.8132 (p90) REVERT: B 48 SER cc_start: 0.8991 (m) cc_final: 0.8511 (t) REVERT: B 103 THR cc_start: 0.8822 (m) cc_final: 0.8543 (p) REVERT: D 6 ASN cc_start: 0.8172 (t0) cc_final: 0.7872 (t0) REVERT: D 37 ASP cc_start: 0.8584 (p0) cc_final: 0.8347 (p0) REVERT: D 74 PHE cc_start: 0.8540 (m-80) cc_final: 0.7893 (m-80) REVERT: F 6 ASN cc_start: 0.8926 (t0) cc_final: 0.8691 (t0) REVERT: H 3 LYS cc_start: 0.4887 (mttt) cc_final: 0.4686 (tptm) REVERT: H 15 GLU cc_start: 0.9017 (tp30) cc_final: 0.8760 (tp30) REVERT: H 85 TYR cc_start: 0.8556 (p90) cc_final: 0.7879 (p90) REVERT: J 18 LEU cc_start: 0.8852 (mm) cc_final: 0.8605 (mm) REVERT: J 45 LEU cc_start: 0.8405 (tp) cc_final: 0.8123 (tp) REVERT: J 55 GLU cc_start: 0.8338 (pm20) cc_final: 0.8034 (mp0) REVERT: J 72 TYR cc_start: 0.8433 (p90) cc_final: 0.8026 (p90) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3456 time to fit residues: 190.0022 Evaluate side-chains 261 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** E 24 ASN ** 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 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27814 Z= 0.246 Angle : 0.656 8.149 40832 Z= 0.338 Chirality : 0.037 0.195 5130 Planarity : 0.005 0.089 2588 Dihedral : 23.844 178.335 12238 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.23), residues: 1356 helix: 0.41 (0.21), residues: 608 sheet: -0.36 (0.33), residues: 254 loop : -1.63 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 58 HIS 0.012 0.002 HIS I 60 PHE 0.017 0.002 PHE B 111 TYR 0.023 0.002 TYR C 196 ARG 0.005 0.001 ARG F 75 *********************** 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 327 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8342 (m-40) cc_final: 0.7994 (m-40) REVERT: A 48 SER cc_start: 0.8960 (m) cc_final: 0.8549 (t) REVERT: A 65 TYR cc_start: 0.7507 (m-10) cc_final: 0.6797 (m-10) REVERT: A 103 THR cc_start: 0.9017 (m) cc_final: 0.8694 (p) REVERT: C 228 LYS cc_start: 0.8916 (mttt) cc_final: 0.8670 (mptt) REVERT: E 18 GLU cc_start: 0.8367 (tp30) cc_final: 0.8105 (tp30) REVERT: G 15 GLU cc_start: 0.8914 (tp30) cc_final: 0.8668 (tp30) REVERT: G 25 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8125 (mt-10) REVERT: G 48 MET cc_start: 0.8642 (mmm) cc_final: 0.8381 (mmm) REVERT: G 78 VAL cc_start: 0.9074 (t) cc_final: 0.8843 (t) REVERT: G 106 GLU cc_start: 0.8493 (mp0) cc_final: 0.8045 (mp0) REVERT: I 45 LEU cc_start: 0.8748 (tp) cc_final: 0.8500 (tp) REVERT: I 72 TYR cc_start: 0.8607 (p90) cc_final: 0.8116 (p90) REVERT: I 81 LEU cc_start: 0.9730 (mt) cc_final: 0.9438 (mt) REVERT: B 48 SER cc_start: 0.9081 (m) cc_final: 0.8743 (t) REVERT: D 6 ASN cc_start: 0.8408 (t0) cc_final: 0.8110 (t0) REVERT: D 74 PHE cc_start: 0.8724 (m-80) cc_final: 0.8035 (m-80) REVERT: F 6 ASN cc_start: 0.8988 (t0) cc_final: 0.8664 (t0) REVERT: F 7 ILE cc_start: 0.9138 (mm) cc_final: 0.8864 (tp) REVERT: F 73 ASP cc_start: 0.9006 (p0) cc_final: 0.8285 (t0) REVERT: F 83 GLU cc_start: 0.8981 (pt0) cc_final: 0.8701 (pm20) REVERT: H 15 GLU cc_start: 0.9055 (tp30) cc_final: 0.8742 (tp30) REVERT: H 48 MET cc_start: 0.8779 (mmm) cc_final: 0.8563 (mtp) REVERT: J 18 LEU cc_start: 0.8790 (mm) cc_final: 0.8580 (mm) REVERT: J 45 LEU cc_start: 0.8462 (tp) cc_final: 0.8166 (tp) REVERT: J 55 GLU cc_start: 0.8361 (pm20) cc_final: 0.8107 (mp0) REVERT: J 72 TYR cc_start: 0.8529 (p90) cc_final: 0.8030 (p90) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.3350 time to fit residues: 178.1627 Evaluate side-chains 253 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27814 Z= 0.259 Angle : 0.684 9.519 40832 Z= 0.351 Chirality : 0.038 0.234 5130 Planarity : 0.006 0.097 2588 Dihedral : 23.957 176.430 12238 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.27 (0.20), residues: 602 sheet: -0.28 (0.33), residues: 240 loop : -1.73 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 58 HIS 0.005 0.001 HIS I 60 PHE 0.022 0.002 PHE A 111 TYR 0.032 0.003 TYR D 176 ARG 0.012 0.001 ARG H 105 *********************** 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 316 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8489 (m-40) cc_final: 0.8202 (m-40) REVERT: A 48 SER cc_start: 0.8992 (m) cc_final: 0.8592 (t) REVERT: A 60 TYR cc_start: 0.7565 (t80) cc_final: 0.7173 (t80) REVERT: A 103 THR cc_start: 0.8993 (m) cc_final: 0.8636 (p) REVERT: C 30 TYR cc_start: 0.8000 (p90) cc_final: 0.7697 (p90) REVERT: E 6 ASN cc_start: 0.8957 (t0) cc_final: 0.8706 (t0) REVERT: E 18 GLU cc_start: 0.8376 (tp30) cc_final: 0.7980 (tp30) REVERT: E 73 ASP cc_start: 0.8266 (t0) cc_final: 0.7742 (t0) REVERT: E 83 GLU cc_start: 0.9086 (pt0) cc_final: 0.8694 (pm20) REVERT: G 3 LYS cc_start: 0.3645 (mttt) cc_final: 0.2647 (tptm) REVERT: G 15 GLU cc_start: 0.8980 (tp30) cc_final: 0.8617 (tp30) REVERT: G 18 ASP cc_start: 0.9139 (m-30) cc_final: 0.8727 (m-30) REVERT: G 25 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8247 (mt-10) REVERT: G 48 MET cc_start: 0.8593 (mmm) cc_final: 0.7954 (tpp) REVERT: I 45 LEU cc_start: 0.8807 (tp) cc_final: 0.8506 (tp) REVERT: I 72 TYR cc_start: 0.8660 (p90) cc_final: 0.8144 (p90) REVERT: B 48 SER cc_start: 0.9073 (m) cc_final: 0.8781 (t) REVERT: B 60 TYR cc_start: 0.7359 (t80) cc_final: 0.7096 (t80) REVERT: B 103 THR cc_start: 0.8877 (m) cc_final: 0.8606 (p) REVERT: F 6 ASN cc_start: 0.9056 (t0) cc_final: 0.8719 (t0) REVERT: F 73 ASP cc_start: 0.9040 (p0) cc_final: 0.8580 (p0) REVERT: F 83 GLU cc_start: 0.8959 (pt0) cc_final: 0.8545 (pm20) REVERT: H 15 GLU cc_start: 0.9055 (tp30) cc_final: 0.8759 (tp30) REVERT: H 23 LEU cc_start: 0.9615 (mm) cc_final: 0.9404 (mm) REVERT: H 48 MET cc_start: 0.9023 (mmm) cc_final: 0.8277 (tpt) REVERT: J 45 LEU cc_start: 0.8554 (tp) cc_final: 0.8113 (tp) REVERT: J 55 GLU cc_start: 0.8360 (pm20) cc_final: 0.8122 (mp0) REVERT: J 72 TYR cc_start: 0.8539 (p90) cc_final: 0.8032 (p90) REVERT: J 81 LEU cc_start: 0.9696 (mt) cc_final: 0.9425 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.3215 time to fit residues: 168.8377 Evaluate side-chains 253 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 169 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 133 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.8900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27814 Z= 0.315 Angle : 0.750 13.983 40832 Z= 0.383 Chirality : 0.040 0.210 5130 Planarity : 0.006 0.091 2588 Dihedral : 24.152 173.646 12238 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.23), residues: 1356 helix: 0.06 (0.20), residues: 586 sheet: -0.42 (0.33), residues: 244 loop : -1.72 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 57 HIS 0.007 0.002 HIS I 60 PHE 0.019 0.003 PHE A 111 TYR 0.029 0.003 TYR A 46 ARG 0.014 0.001 ARG H 105 *********************** 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 317 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.9068 (m) cc_final: 0.8697 (t) REVERT: A 60 TYR cc_start: 0.7618 (t80) cc_final: 0.7207 (t80) REVERT: A 103 THR cc_start: 0.9044 (m) cc_final: 0.8655 (p) REVERT: C 30 TYR cc_start: 0.8152 (p90) cc_final: 0.7918 (p90) REVERT: C 37 ASP cc_start: 0.8774 (p0) cc_final: 0.8562 (p0) REVERT: C 202 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7995 (tp30) REVERT: E 18 GLU cc_start: 0.8237 (tp30) cc_final: 0.7935 (tp30) REVERT: E 73 ASP cc_start: 0.7956 (t0) cc_final: 0.7726 (t0) REVERT: E 83 GLU cc_start: 0.8999 (pt0) cc_final: 0.8590 (pm20) REVERT: G 3 LYS cc_start: 0.3366 (mttt) cc_final: 0.3145 (mttt) REVERT: G 15 GLU cc_start: 0.8997 (tp30) cc_final: 0.8653 (tp30) REVERT: G 18 ASP cc_start: 0.9193 (m-30) cc_final: 0.8815 (m-30) REVERT: G 25 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8526 (mt-10) REVERT: G 56 LYS cc_start: 0.9229 (mttt) cc_final: 0.9026 (mmtp) REVERT: I 45 LEU cc_start: 0.8922 (tp) cc_final: 0.8595 (tp) REVERT: I 72 TYR cc_start: 0.8772 (p90) cc_final: 0.8161 (p90) REVERT: B 24 LEU cc_start: 0.8235 (tp) cc_final: 0.7892 (tp) REVERT: B 48 SER cc_start: 0.9036 (m) cc_final: 0.8720 (t) REVERT: D 4 ASP cc_start: 0.7800 (t70) cc_final: 0.6598 (t70) REVERT: D 6 ASN cc_start: 0.8444 (t0) cc_final: 0.7858 (m-40) REVERT: D 170 THR cc_start: 0.9200 (p) cc_final: 0.8963 (p) REVERT: D 181 PRO cc_start: 0.9312 (Cg_endo) cc_final: 0.9066 (Cg_exo) REVERT: F 6 ASN cc_start: 0.9061 (t0) cc_final: 0.8702 (t0) REVERT: F 83 GLU cc_start: 0.8895 (pt0) cc_final: 0.8526 (pm20) REVERT: H 48 MET cc_start: 0.9026 (mmm) cc_final: 0.8495 (tpp) REVERT: H 85 TYR cc_start: 0.8816 (p90) cc_final: 0.8536 (p90) REVERT: J 55 GLU cc_start: 0.8347 (pm20) cc_final: 0.8104 (mp0) REVERT: J 72 TYR cc_start: 0.8537 (p90) cc_final: 0.8147 (p90) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.3235 time to fit residues: 170.4229 Evaluate side-chains 245 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 169 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.8974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27814 Z= 0.214 Angle : 0.669 11.708 40832 Z= 0.344 Chirality : 0.038 0.219 5130 Planarity : 0.005 0.093 2588 Dihedral : 24.021 171.970 12238 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.23), residues: 1356 helix: 0.13 (0.20), residues: 600 sheet: -0.57 (0.33), residues: 252 loop : -1.50 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 57 HIS 0.006 0.002 HIS F 10 PHE 0.027 0.002 PHE C 151 TYR 0.026 0.002 TYR C 176 ARG 0.010 0.001 ARG H 105 ********************** 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 312 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.908 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 48 SER cc_start: 0.8864 (m) cc_final: 0.8501 (t) REVERT: E 18 GLU cc_start: 0.8117 (tp30) cc_final: 0.7825 (tp30) REVERT: E 83 GLU cc_start: 0.8997 (pt0) cc_final: 0.8668 (pm20) REVERT: G 3 LYS cc_start: 0.3327 (mttt) cc_final: 0.3119 (mttt) REVERT: G 15 GLU cc_start: 0.8878 (tp30) cc_final: 0.8625 (tp30) REVERT: G 18 ASP cc_start: 0.9265 (m-30) cc_final: 0.8819 (m-30) REVERT: G 25 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8493 (mt-10) REVERT: G 48 MET cc_start: 0.8118 (tpt) cc_final: 0.7315 (tmm) REVERT: G 56 LYS cc_start: 0.9264 (mttt) cc_final: 0.9023 (mmtp) REVERT: G 106 GLU cc_start: 0.8155 (mp0) cc_final: 0.7949 (mp0) REVERT: I 60 HIS cc_start: 0.7951 (p-80) cc_final: 0.7662 (p-80) REVERT: I 72 TYR cc_start: 0.8616 (p90) cc_final: 0.8172 (p90) REVERT: B 48 SER cc_start: 0.9041 (m) cc_final: 0.8743 (t) REVERT: B 60 TYR cc_start: 0.7574 (t80) cc_final: 0.7163 (t80) REVERT: B 76 ASP cc_start: 0.8942 (m-30) cc_final: 0.8687 (m-30) REVERT: B 103 THR cc_start: 0.9152 (m) cc_final: 0.8832 (p) REVERT: D 4 ASP cc_start: 0.7900 (t70) cc_final: 0.6245 (t70) REVERT: D 6 ASN cc_start: 0.8306 (t0) cc_final: 0.7561 (m-40) REVERT: D 138 LEU cc_start: 0.8770 (mm) cc_final: 0.8363 (mm) REVERT: D 170 THR cc_start: 0.9229 (p) cc_final: 0.8910 (p) REVERT: D 181 PRO cc_start: 0.9261 (Cg_endo) cc_final: 0.8990 (Cg_exo) REVERT: F 6 ASN cc_start: 0.8936 (t0) cc_final: 0.8645 (t0) REVERT: F 73 ASP cc_start: 0.9160 (p0) cc_final: 0.8873 (p0) REVERT: F 83 GLU cc_start: 0.8969 (pt0) cc_final: 0.8648 (pm20) REVERT: H 15 GLU cc_start: 0.8938 (tp30) cc_final: 0.8648 (tp30) REVERT: H 85 TYR cc_start: 0.8812 (p90) cc_final: 0.8491 (p90) REVERT: J 45 LEU cc_start: 0.8655 (tp) cc_final: 0.8223 (tp) REVERT: J 55 GLU cc_start: 0.8251 (pm20) cc_final: 0.8005 (mp0) REVERT: J 72 TYR cc_start: 0.8448 (p90) cc_final: 0.7939 (p90) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3260 time to fit residues: 167.9502 Evaluate side-chains 256 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 0.0980 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.081782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.061702 restraints weight = 193639.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063045 restraints weight = 107526.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064084 restraints weight = 76599.636| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.9009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27814 Z= 0.181 Angle : 0.631 11.032 40832 Z= 0.326 Chirality : 0.036 0.206 5130 Planarity : 0.005 0.092 2588 Dihedral : 23.838 172.261 12238 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -0.88 (0.23), residues: 1356 helix: 0.25 (0.21), residues: 600 sheet: -0.47 (0.33), residues: 258 loop : -1.59 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 57 HIS 0.007 0.001 HIS F 10 PHE 0.021 0.002 PHE C 151 TYR 0.028 0.002 TYR E 93 ARG 0.010 0.001 ARG H 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.04 seconds wall clock time: 91 minutes 15.23 seconds (5475.23 seconds total)