Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 05:41:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/07_2023/7qiy_14003_trim_updated.pdb" } resolution = 2.58 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= -0.001 sd= 0.004 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: 9 Type Number sf(0) Gaussians K 10 8.98 5 Zn 1 6.06 5 P 491 5.49 5 Mg 28 5.21 5 S 67 5.16 5 C 13400 2.51 5 N 4405 2.21 5 O 6161 1.98 5 H 19242 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 43805 Number of models: 1 Model: "" Number of chains: 31 Chain: "2" Number of atoms: 14904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 14904 Classifications: {'RNA': 474} Modifications used: {'rna2p': 3, 'rna2p_pur': 30, 'rna2p_pyr': 44, 'rna3p': 22, 'rna3p_pur': 199, 'rna3p_pyr': 174} Link IDs: {'rna2p': 77, 'rna3p': 396} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3429 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2965 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1572 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "G" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2096 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 9, 'TRANS': 116} Chain: "H" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2339 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 134} Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1420 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "J" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2343 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "K" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2208 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "L" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1701 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "M" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1070 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 805 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4898 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 6, 'TRANS': 310} Chain breaks: 1 Chain: "P" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1228 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 451 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna3p': 13} Chain: "R" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Classifications: {'RNA': 3} Modifications used: {'3*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 40 Unusual residues: {' K': 7, ' MG': 27, 'PUT': 1} Classifications: {'undetermined': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36267 SG CYS N 21 69.305 47.586 69.295 1.00 15.44 S ATOM 36317 SG CYS N 24 67.022 45.052 68.387 1.00 16.87 S ATOM 36548 SG CYS N 39 65.660 47.994 70.628 1.00 12.68 S ATOM 36599 SG CYS N 42 67.641 45.482 72.063 1.00 13.24 S Time building chain proxies: 16.70, per 1000 atoms: 0.38 Number of scatterers: 43805 At special positions: 0 Unit cell: (122.84, 136.12, 165.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 K 10 19.00 S 67 16.00 P 491 15.00 Mg 28 11.99 O 6161 8.00 N 4405 7.00 C 13400 6.00 H 19242 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 37.43 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 102 " pdb="ZN ZN N 102 " - pdb=" SG CYS N 39 " pdb="ZN ZN N 102 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 102 " - pdb=" SG CYS N 42 " pdb="ZN ZN N 102 " - pdb=" SG CYS N 21 " Number of angles added : 6 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 22 sheets defined 33.9% alpha, 18.4% beta 132 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 26.07 Creating SS restraints... Processing helix chain 'D' and resid 10 through 31 Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 58 through 62 removed outlier: 4.131A pdb=" N LEU D 62 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 79 removed outlier: 6.111A pdb=" N ARG D 68 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 69 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 72 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 75 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.599A pdb=" N TYR D 170 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 119 through 130 Processing helix chain 'E' and resid 154 through 173 Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 199 through 214 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 39 through 51 Processing helix chain 'F' and resid 70 through 80 removed outlier: 3.607A pdb=" N THR F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.871A pdb=" N ASP G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 42 removed outlier: 3.925A pdb=" N LYS G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 52 Processing helix chain 'G' and resid 57 through 72 removed outlier: 3.528A pdb=" N LYS G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 115 through 117 No H-bonds generated for 'chain 'G' and resid 115 through 117' Processing helix chain 'G' and resid 122 through 125 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 49 through 52 No H-bonds generated for 'chain 'H' and resid 49 through 52' Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 78 through 100 removed outlier: 3.660A pdb=" N ILE H 82 " --> pdb=" O HIS H 78 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 116 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'I' and resid 7 through 19 Processing helix chain 'I' and resid 28 through 38 removed outlier: 3.646A pdb=" N LYS I 33 " --> pdb=" O HIS I 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU I 36 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 63 removed outlier: 3.554A pdb=" N LYS I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 Processing helix chain 'J' and resid 26 through 32 removed outlier: 4.057A pdb=" N THR J 31 " --> pdb=" O MET J 27 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER J 32 " --> pdb=" O PHE J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 47 Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 61 through 72 removed outlier: 3.753A pdb=" N MET J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 101 through 116 Processing helix chain 'J' and resid 120 through 127 Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 12 through 26 Processing helix chain 'K' and resid 53 through 67 Processing helix chain 'K' and resid 73 through 79 Processing helix chain 'K' and resid 98 through 110 Processing helix chain 'K' and resid 126 through 138 Processing helix chain 'L' and resid 33 through 48 Processing helix chain 'L' and resid 99 through 106 Processing helix chain 'N' and resid 33 through 35 No H-bonds generated for 'chain 'N' and resid 33 through 35' Processing helix chain 'N' and resid 40 through 50 removed outlier: 5.131A pdb=" N LYS N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU N 49 " --> pdb=" O SER N 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 276 through 282 Processing helix chain 'P' and resid 45 through 57 Proline residue: P 56 - end of helix Processing helix chain 'P' and resid 63 through 69 Processing helix chain 'P' and resid 74 through 86 Processing sheet with id= A, first strand: chain 'D' and resid 87 through 92 removed outlier: 6.555A pdb=" N THR D 49 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR D 90 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 51 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU D 92 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 53 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 39 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 151 through 158 removed outlier: 3.524A pdb=" N GLY D 136 " --> pdb=" O MET D 192 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 134 through 137 Processing sheet with id= D, first strand: chain 'F' and resid 20 through 24 Processing sheet with id= E, first strand: chain 'G' and resid 82 through 84 Processing sheet with id= F, first strand: chain 'H' and resid 10 through 17 Processing sheet with id= G, first strand: chain 'J' and resid 12 through 15 Processing sheet with id= H, first strand: chain 'K' and resid 82 through 84 Processing sheet with id= I, first strand: chain 'K' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'L' and resid 89 through 97 Processing sheet with id= K, first strand: chain 'L' and resid 63 through 70 Processing sheet with id= L, first strand: chain 'M' and resid 51 through 54 removed outlier: 6.625A pdb=" N ARG M 27 " --> pdb=" O ILE M 11 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE M 13 " --> pdb=" O GLN M 25 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN M 25 " --> pdb=" O ILE M 13 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 15 through 17 removed outlier: 3.539A pdb=" N GLY M 15 " --> pdb=" O GLN M 25 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 19 through 24 removed outlier: 6.660A pdb=" N SER O 35 " --> pdb=" O THR O 20 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE O 22 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL O 33 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE O 32 " --> pdb=" O TRP O 44 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N SER O 45 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 67 through 72 removed outlier: 6.615A pdb=" N GLY O 82 " --> pdb=" O GLU O 68 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL O 70 " --> pdb=" O LEU O 80 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU O 80 " --> pdb=" O VAL O 70 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU O 72 " --> pdb=" O PHE O 78 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE O 78 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG O 100 " --> pdb=" O LEU O 90 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP O 92 " --> pdb=" O THR O 98 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N THR O 98 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'O' and resid 140 through 143 removed outlier: 4.220A pdb=" N ILE O 130 " --> pdb=" O ILE O 143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER O 111 " --> pdb=" O ALA O 124 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'O' and resid 155 through 158 removed outlier: 3.935A pdb=" N CYS O 155 " --> pdb=" O GLY O 170 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN O 180 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU O 186 " --> pdb=" O ASN O 180 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 241 through 243 removed outlier: 3.874A pdb=" N VAL O 270 " --> pdb=" O ILE O 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP O 262 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE O 268 " --> pdb=" O ASP O 262 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 5 through 12 removed outlier: 3.720A pdb=" N SER O 5 " --> pdb=" O GLY O 324 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL O 320 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR O 11 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE O 318 " --> pdb=" O THR O 11 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 197 through 202 removed outlier: 7.030A pdb=" N GLY O 212 " --> pdb=" O ASN O 198 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL O 200 " --> pdb=" O ALA O 210 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA O 210 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 217 through 222 removed outlier: 3.690A pdb=" N TYR O 230 " --> pdb=" O LEU O 220 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP O 222 " --> pdb=" O LYS O 228 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS O 228 " --> pdb=" O ASP O 222 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 90 through 95 removed outlier: 6.723A pdb=" N ILE P 101 " --> pdb=" O VAL P 93 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 330 hydrogen bonds 536 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 22.14 Time building geometry restraints manager: 38.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19222 1.03 - 1.23: 179 1.23 - 1.42: 11884 1.42 - 1.61: 13602 1.61 - 1.81: 109 Bond restraints: 44996 Sorted by residual: bond pdb=" C2' A2M 21328 " pdb=" C1' A2M 21328 " ideal model delta sigma weight residual 1.305 1.532 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2' A2M 21578 " pdb=" C1' A2M 21578 " ideal model delta sigma weight residual 1.305 1.523 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" O4' A2M 21578 " pdb=" C1' A2M 21578 " ideal model delta sigma weight residual 1.615 1.414 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" O4' A2M 21328 " pdb=" C1' A2M 21328 " ideal model delta sigma weight residual 1.615 1.419 0.196 2.00e-02 2.50e+03 9.59e+01 bond pdb=" N1 I2T 21194 " pdb=" C6 I2T 21194 " ideal model delta sigma weight residual 1.547 1.362 0.185 2.00e-02 2.50e+03 8.53e+01 ... (remaining 44991 not shown) Histogram of bond angle deviations from ideal: 78.93 - 89.94: 12 89.94 - 100.96: 56 100.96 - 111.97: 50067 111.97 - 122.98: 25032 122.98 - 134.00: 5723 Bond angle restraints: 80890 Sorted by residual: angle pdb=" C1' A2M 21328 " pdb=" N9 A2M 21328 " pdb=" C8 A2M 21328 " ideal model delta sigma weight residual 88.50 127.11 -38.61 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C1' A2M 21578 " pdb=" N9 A2M 21578 " pdb=" C8 A2M 21578 " ideal model delta sigma weight residual 88.50 126.69 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb="HG22 THR G 84 " pdb=" CG2 THR G 84 " pdb="HG23 THR G 84 " ideal model delta sigma weight residual 109.00 78.93 30.07 3.00e+00 1.11e-01 1.00e+02 angle pdb="HG21 THR G 84 " pdb=" CG2 THR G 84 " pdb="HG23 THR G 84 " ideal model delta sigma weight residual 109.00 79.06 29.94 3.00e+00 1.11e-01 9.96e+01 angle pdb=" CG LEU F 45 " pdb=" CD2 LEU F 45 " pdb="HD22 LEU F 45 " ideal model delta sigma weight residual 109.00 79.19 29.81 3.00e+00 1.11e-01 9.87e+01 ... (remaining 80885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 17519 35.49 - 70.98: 314 70.98 - 106.47: 30 106.47 - 141.97: 1 141.97 - 177.46: 6 Dihedral angle restraints: 17870 sinusoidal: 12148 harmonic: 5722 Sorted by residual: dihedral pdb=" O4' C 21376 " pdb=" C1' C 21376 " pdb=" N1 C 21376 " pdb=" C2 C 21376 " ideal model delta sinusoidal sigma weight residual -128.00 49.46 -177.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 21476 " pdb=" C1' C 21476 " pdb=" N1 C 21476 " pdb=" C2 C 21476 " ideal model delta sinusoidal sigma weight residual 232.00 55.55 176.45 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 21377 " pdb=" C1' C 21377 " pdb=" N1 C 21377 " pdb=" C2 C 21377 " ideal model delta sinusoidal sigma weight residual 232.00 56.58 175.42 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 17867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4185 0.064 - 0.127: 300 0.127 - 0.191: 24 0.191 - 0.254: 0 0.254 - 0.318: 2 Chirality restraints: 4511 Sorted by residual: chirality pdb=" C2' A2M 21328 " pdb=" C3' A2M 21328 " pdb=" O2' A2M 21328 " pdb=" C1' A2M 21328 " both_signs ideal model delta sigma weight residual False -2.39 -2.71 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C2' A2M 21578 " pdb=" C3' A2M 21578 " pdb=" O2' A2M 21578 " pdb=" C1' A2M 21578 " both_signs ideal model delta sigma weight residual False -2.39 -2.68 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1* PSU 21210 " pdb=" O4* PSU 21210 " pdb=" C2* PSU 21210 " pdb=" C5 PSU 21210 " both_signs ideal model delta sigma weight residual False 2.60 2.43 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 4508 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 21218 " 0.033 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' OMC 21218 " 0.437 2.00e-02 2.50e+03 pdb=" O4' OMC 21218 " 0.660 2.00e-02 2.50e+03 pdb=" C3' OMC 21218 " -0.591 2.00e-02 2.50e+03 pdb=" O3' OMC 21218 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMC 21218 " -0.213 2.00e-02 2.50e+03 pdb=" O2' OMC 21218 " 0.906 2.00e-02 2.50e+03 pdb=" C1' OMC 21218 " 0.222 2.00e-02 2.50e+03 pdb=" N1 OMC 21218 " -0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 21274 " -0.035 2.00e-02 2.50e+03 5.68e-01 7.27e+03 pdb=" C4' OMG 21274 " -0.437 2.00e-02 2.50e+03 pdb=" O4' OMG 21274 " -0.622 2.00e-02 2.50e+03 pdb=" C3' OMG 21274 " 0.586 2.00e-02 2.50e+03 pdb=" O3' OMG 21274 " 0.570 2.00e-02 2.50e+03 pdb=" C2' OMG 21274 " 0.206 2.00e-02 2.50e+03 pdb=" O2' OMG 21274 " -0.905 2.00e-02 2.50e+03 pdb=" C1' OMG 21274 " -0.227 2.00e-02 2.50e+03 pdb=" N9 OMG 21274 " 0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 21432 " 0.003 2.00e-02 2.50e+03 5.65e-01 7.18e+03 pdb=" C4' OMG 21432 " -0.443 2.00e-02 2.50e+03 pdb=" O4' OMG 21432 " -0.726 2.00e-02 2.50e+03 pdb=" C3' OMG 21432 " 0.578 2.00e-02 2.50e+03 pdb=" O3' OMG 21432 " 0.502 2.00e-02 2.50e+03 pdb=" C2' OMG 21432 " 0.248 2.00e-02 2.50e+03 pdb=" O2' OMG 21432 " -0.823 2.00e-02 2.50e+03 pdb=" C1' OMG 21432 " -0.220 2.00e-02 2.50e+03 pdb=" N9 OMG 21432 " 0.880 2.00e-02 2.50e+03 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.28: 6779 2.28 - 2.99: 106679 2.99 - 3.71: 163804 3.71 - 4.42: 254561 4.42 - 5.14: 369872 Nonbonded interactions: 901695 Sorted by model distance: nonbonded pdb=" OP1 A 21491 " pdb=" HH TYR N 34 " model vdw 1.565 1.850 nonbonded pdb=" O ASP O 262 " pdb=" H LYS O 266 " model vdw 1.594 1.850 nonbonded pdb=" OP2 A 21331 " pdb=" HG SER D 163 " model vdw 1.596 1.850 nonbonded pdb=" OE2 GLU D 26 " pdb=" HE ARG D 30 " model vdw 1.615 1.850 nonbonded pdb=" OP2 A 21522 " pdb=" HZ2 LYS L 63 " model vdw 1.628 1.850 ... (remaining 901690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 9.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 35.400 Check model and map are aligned: 0.630 Set scattering table: 0.340 Process input model: 174.110 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.008 0.227 25754 Z= 0.459 Angle : 0.739 38.607 37076 Z= 0.324 Chirality : 0.037 0.318 4511 Planarity : 0.021 0.577 2901 Dihedral : 13.019 177.456 11210 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 0.57 (0.20), residues: 1700 helix: 0.74 (0.21), residues: 582 sheet: 0.16 (0.29), residues: 313 loop : 0.38 (0.22), residues: 805 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.747 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: 348 average time/residue: 3.7590 time to fit residues: 1455.9515 Evaluate side-chains 278 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN O 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 25754 Z= 0.373 Angle : 0.762 16.794 37076 Z= 0.404 Chirality : 0.044 0.258 4511 Planarity : 0.007 0.135 2901 Dihedral : 13.154 178.185 7714 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 0.78 (0.20), residues: 1700 helix: 1.17 (0.21), residues: 583 sheet: 0.36 (0.29), residues: 311 loop : 0.23 (0.22), residues: 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 297 average time/residue: 3.2469 time to fit residues: 1088.6281 Evaluate side-chains 287 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.726 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.5038 time to fit residues: 7.5030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25754 Z= 0.185 Angle : 0.654 15.700 37076 Z= 0.355 Chirality : 0.038 0.230 4511 Planarity : 0.006 0.127 2901 Dihedral : 12.989 178.699 7714 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.12 (0.20), residues: 1700 helix: 1.64 (0.21), residues: 583 sheet: 0.46 (0.29), residues: 314 loop : 0.32 (0.22), residues: 803 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 299 average time/residue: 3.3026 time to fit residues: 1115.0243 Evaluate side-chains 292 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 280 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.5185 time to fit residues: 7.8068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 0.0000 chunk 209 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 25754 Z= 0.173 Angle : 0.641 15.648 37076 Z= 0.349 Chirality : 0.037 0.244 4511 Planarity : 0.006 0.125 2901 Dihedral : 12.930 179.088 7714 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.33 (0.21), residues: 1700 helix: 1.89 (0.21), residues: 585 sheet: 0.51 (0.29), residues: 315 loop : 0.40 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 291 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 300 average time/residue: 3.3986 time to fit residues: 1147.6995 Evaluate side-chains 293 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.5812 time to fit residues: 9.3101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 25754 Z= 0.150 Angle : 0.625 15.675 37076 Z= 0.341 Chirality : 0.036 0.241 4511 Planarity : 0.005 0.123 2901 Dihedral : 12.866 179.337 7714 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.47 (0.21), residues: 1700 helix: 2.12 (0.22), residues: 583 sheet: 0.46 (0.28), residues: 319 loop : 0.45 (0.23), residues: 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 296 average time/residue: 3.2941 time to fit residues: 1103.5571 Evaluate side-chains 291 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 281 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.6093 time to fit residues: 5.9902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 25754 Z= 0.225 Angle : 0.664 16.073 37076 Z= 0.358 Chirality : 0.038 0.222 4511 Planarity : 0.006 0.129 2901 Dihedral : 12.907 179.480 7714 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.47 (0.21), residues: 1700 helix: 2.06 (0.21), residues: 584 sheet: 0.57 (0.28), residues: 315 loop : 0.45 (0.23), residues: 801 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 291 average time/residue: 3.3266 time to fit residues: 1090.0474 Evaluate side-chains 292 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 278 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.7859 time to fit residues: 11.3722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25754 Z= 0.211 Angle : 0.658 15.927 37076 Z= 0.355 Chirality : 0.038 0.230 4511 Planarity : 0.006 0.128 2901 Dihedral : 12.905 179.624 7714 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.50 (0.21), residues: 1700 helix: 2.09 (0.21), residues: 585 sheet: 0.55 (0.28), residues: 317 loop : 0.47 (0.23), residues: 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 289 average time/residue: 3.3015 time to fit residues: 1075.3996 Evaluate side-chains 292 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 280 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.9504 time to fit residues: 9.8481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 25754 Z= 0.235 Angle : 0.674 16.108 37076 Z= 0.363 Chirality : 0.039 0.224 4511 Planarity : 0.006 0.130 2901 Dihedral : 12.944 179.758 7714 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.54 (0.21), residues: 1700 helix: 2.18 (0.21), residues: 578 sheet: 0.61 (0.29), residues: 310 loop : 0.44 (0.22), residues: 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 280 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 290 average time/residue: 3.2525 time to fit residues: 1063.9798 Evaluate side-chains 288 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 277 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.1767 time to fit residues: 7.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 148 GLN O 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 25754 Z= 0.283 Angle : 0.704 16.343 37076 Z= 0.376 Chirality : 0.040 0.222 4511 Planarity : 0.006 0.133 2901 Dihedral : 13.010 179.898 7714 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.46 (0.21), residues: 1700 helix: 2.11 (0.21), residues: 577 sheet: 0.57 (0.28), residues: 318 loop : 0.40 (0.23), residues: 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 284 average time/residue: 3.3217 time to fit residues: 1064.3186 Evaluate side-chains 289 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.8436 time to fit residues: 11.9857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 148 GLN J 16 GLN O 164 GLN O 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 25754 Z= 0.229 Angle : 0.683 16.026 37076 Z= 0.367 Chirality : 0.039 0.229 4511 Planarity : 0.006 0.129 2901 Dihedral : 12.992 179.910 7714 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.49 (0.21), residues: 1700 helix: 2.15 (0.21), residues: 577 sheet: 0.57 (0.28), residues: 318 loop : 0.42 (0.23), residues: 805 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 173 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 274 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 283 average time/residue: 3.3329 time to fit residues: 1064.7659 Evaluate side-chains 284 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.4857 time to fit residues: 4.8895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 158 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.089866 restraints weight = 63192.182| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 0.98 r_work: 0.2747 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 25754 Z= 0.140 Angle : 0.654 15.694 37076 Z= 0.356 Chirality : 0.037 0.243 4511 Planarity : 0.006 0.122 2901 Dihedral : 12.958 179.918 7714 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.06 % 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: 1.58 (0.21), residues: 1700 helix: 2.28 (0.22), residues: 577 sheet: 0.51 (0.28), residues: 319 loop : 0.47 (0.23), residues: 804 =============================================================================== Job complete usr+sys time: 19489.62 seconds wall clock time: 342 minutes 30.16 seconds (20550.16 seconds total)