Starting phenix.real_space_refine (version: dev) on Sat Feb 25 16:28:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/02_2023/6k0b_9900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/02_2023/6k0b_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_9900/02_2023/6k0b_9900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/02_2023/6k0b_9900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/02_2023/6k0b_9900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0b_9900/02_2023/6k0b_9900.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 105": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 14.76, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 12.30 Conformation dependent library (CDL) restraints added in 1.9 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: 8.27 Time building geometry restraints manager: 12.93 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: 99.82 - 106.69: 4180 106.69 - 113.55: 16335 113.55 - 120.42: 10708 120.42 - 127.28: 8122 127.28 - 134.15: 1487 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: 14790 34.82 - 69.64: 526 69.64 - 104.46: 52 104.46 - 139.28: 0 139.28 - 174.10: 4 Dihedral angle restraints: 15372 sinusoidal: 11318 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 15369 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 2.440 nonbonded pdb=" NZ LYS G 114 " pdb=" OP1 G X 125 " model vdw 2.077 2.520 nonbonded pdb=" NH2 ARG H 60 " pdb=" OP1 U Y 161 " model vdw 2.100 2.520 nonbonded pdb=" OG1 THR F 41 " pdb=" OP1 A Y 75 " model vdw 2.120 2.440 nonbonded pdb=" N2 G Y 223 " pdb=" OP2 A Y 226 " model vdw 2.153 2.520 ... (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 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 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. 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.930 Check model and map are aligned: 0.410 Process input model: 75.400 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 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 : 14.207 174.099 12748 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.66 % 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 *********************** 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 : 2.087 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 outliers start: 8 outliers final: 2 residues processed: 725 average time/residue: 0.4868 time to fit residues: 520.5525 Evaluate side-chains 345 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2501 time to fit residues: 3.3123 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 60 optimal weight: 0.0370 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 overall best weight: 5.3264 ------------------------------------------------------------------------------- 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** C 133 ASN C 180 ASN C 189 ASN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN B 36 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 154 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 27814 Z= 0.462 Angle : 0.955 14.846 40832 Z= 0.478 Chirality : 0.044 0.346 5130 Planarity : 0.007 0.072 2588 Dihedral : 15.670 177.984 9706 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer Outliers : 0.41 % 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: -2.02 (0.22), residues: 1356 helix: -0.80 (0.19), residues: 592 sheet: -1.09 (0.32), residues: 246 loop : -1.95 (0.27), residues: 518 *********************** 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 382 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 377 time to evaluate : 1.998 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 outliers start: 5 outliers final: 1 residues processed: 380 average time/residue: 0.3832 time to fit residues: 226.6430 Evaluate side-chains 263 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2185 time to fit residues: 2.7535 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 27814 Z= 0.185 Angle : 0.606 8.718 40832 Z= 0.312 Chirality : 0.034 0.220 5130 Planarity : 0.005 0.066 2588 Dihedral : 15.247 177.579 9706 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.16 % 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: -1.20 (0.23), residues: 1356 helix: -0.09 (0.21), residues: 602 sheet: -0.45 (0.32), residues: 244 loop : -1.73 (0.28), residues: 510 *********************** 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 381 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 379 time to evaluate : 1.868 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 outliers start: 2 outliers final: 1 residues processed: 379 average time/residue: 0.3718 time to fit residues: 219.5247 Evaluate side-chains 288 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2718 time to fit residues: 2.7638 ------------------------------------------------------------------------------- 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: 9.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 27814 Z= 0.286 Angle : 0.706 12.471 40832 Z= 0.359 Chirality : 0.038 0.506 5130 Planarity : 0.006 0.066 2588 Dihedral : 15.457 178.625 9706 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 0.57 % 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: -1.05 (0.22), residues: 1356 helix: 0.16 (0.21), residues: 586 sheet: -0.38 (0.34), residues: 242 loop : -1.77 (0.27), residues: 528 *********************** 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 350 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 343 time to evaluate : 2.523 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 outliers start: 7 outliers final: 2 residues processed: 346 average time/residue: 0.3413 time to fit residues: 192.0181 Evaluate side-chains 243 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2709 time to fit residues: 2.9105 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** C 126 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** ** 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: 0.7826 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.108 27814 Z= 0.292 Angle : 0.684 9.239 40832 Z= 0.351 Chirality : 0.037 0.246 5130 Planarity : 0.006 0.071 2588 Dihedral : 15.559 176.201 9706 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.52 % Favored : 92.40 % Rotamer Outliers : 0.16 % 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: -0.98 (0.23), residues: 1356 helix: 0.18 (0.21), residues: 598 sheet: -0.35 (0.34), residues: 240 loop : -1.71 (0.27), residues: 518 *********************** 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 330 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 328 time to evaluate : 1.895 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 outliers start: 2 outliers final: 2 residues processed: 330 average time/residue: 0.3579 time to fit residues: 188.0571 Evaluate side-chains 248 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2936 time to fit residues: 3.1474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** F 10 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.8570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 27814 Z= 0.368 Angle : 0.786 11.853 40832 Z= 0.402 Chirality : 0.041 0.350 5130 Planarity : 0.007 0.096 2588 Dihedral : 16.174 175.007 9706 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 32.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.11 % Favored : 91.74 % Rotamer Outliers : 0.33 % 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: -1.48 (0.22), residues: 1356 helix: -0.23 (0.20), residues: 590 sheet: -0.92 (0.31), residues: 256 loop : -1.79 (0.27), residues: 510 *********************** 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 314 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.3609 time to fit residues: 183.2616 Evaluate side-chains 225 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3594 time to fit residues: 2.7877 ------------------------------------------------------------------------------- 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: 0.7980 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** I 60 HIS ** D 126 HIS ** 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: 0.7838 moved from start: 0.8436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 27814 Z= 0.186 Angle : 0.637 10.196 40832 Z= 0.327 Chirality : 0.037 0.348 5130 Planarity : 0.005 0.069 2588 Dihedral : 15.681 171.050 9706 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.00 % 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: -0.92 (0.23), residues: 1356 helix: 0.24 (0.21), residues: 600 sheet: -0.60 (0.31), residues: 264 loop : -1.57 (0.29), residues: 492 *********************** 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 317 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.948 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 outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.3616 time to fit residues: 185.6772 Evaluate side-chains 244 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2245 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.8600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 27814 Z= 0.212 Angle : 0.647 10.203 40832 Z= 0.333 Chirality : 0.037 0.254 5130 Planarity : 0.005 0.093 2588 Dihedral : 15.577 170.543 9706 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.15 % Favored : 92.63 % Rotamer Outliers : 0.00 % 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: -0.92 (0.23), residues: 1356 helix: 0.22 (0.21), residues: 600 sheet: -0.68 (0.31), residues: 266 loop : -1.49 (0.29), residues: 490 *********************** 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 298 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.975 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 outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3444 time to fit residues: 168.0329 Evaluate side-chains 238 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9872 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN D 133 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 27814 Z= 0.370 Angle : 0.797 13.638 40832 Z= 0.405 Chirality : 0.041 0.224 5130 Planarity : 0.007 0.091 2588 Dihedral : 16.248 171.198 9706 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 34.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.41 % Favored : 91.45 % Rotamer Outliers : 0.00 % 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: -1.50 (0.22), residues: 1356 helix: -0.23 (0.20), residues: 592 sheet: -0.90 (0.32), residues: 254 loop : -1.85 (0.27), residues: 510 *********************** 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 283 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3414 time to fit residues: 157.0051 Evaluate side-chains 226 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1768 ------------------------------------------------------------------------------- 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: 0.8980 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 158 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 30.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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** I 60 HIS ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.9147 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= 0.168 Angle : 0.646 10.584 40832 Z= 0.332 Chirality : 0.037 0.243 5130 Planarity : 0.005 0.085 2588 Dihedral : 15.647 170.899 9706 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 0.00 % 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: -0.83 (0.23), residues: 1356 helix: 0.37 (0.21), residues: 588 sheet: -0.65 (0.32), residues: 266 loop : -1.49 (0.29), residues: 502 ********************** 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 305 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.3322 time to fit residues: 166.5923 Evaluate side-chains 246 residues out of total 1218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1079 ------------------------------------------------------------------------------- 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: 4.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 0.0170 chunk 9 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.080372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059101 restraints weight = 180585.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060588 restraints weight = 100997.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061734 restraints weight = 71092.547| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.9122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 27814 Z= 0.162 Angle : 0.624 9.092 40832 Z= 0.320 Chirality : 0.035 0.219 5130 Planarity : 0.005 0.088 2588 Dihedral : 15.357 170.451 9706 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.00 % 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: -0.69 (0.23), residues: 1356 helix: 0.42 (0.21), residues: 586 sheet: -0.47 (0.33), residues: 264 loop : -1.39 (0.30), residues: 506 =============================================================================== Job complete usr+sys time: 4738.04 seconds wall clock time: 88 minutes 31.66 seconds (5311.66 seconds total)