Starting phenix.real_space_refine on Sat Feb 24 12:49:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_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_14003/02_2024/7qiy_14003_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qiy_14003/02_2024/7qiy_14003_trim_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-dev-5238/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 dihedrals: 3 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: 20.79, per 1000 atoms: 0.47 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: 38.95 Conformation dependent library (CDL) restraints added in 3.1 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: 33.33 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: 27.46 Time building geometry restraints manager: 39.91 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: 20240 35.49 - 70.98: 1374 70.98 - 106.47: 169 106.47 - 141.97: 1 141.97 - 177.46: 6 Dihedral angle restraints: 21790 sinusoidal: 16068 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 21787 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: 8.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.650 Extract box with map and model: 33.960 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 203.730 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 264.000 ------------------------------------------------------------------------------- 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 : 20.303 177.456 13087 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 % Allowed : 3.00 % Favored : 97.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 82 HIS 0.003 0.001 HIS J 120 PHE 0.009 0.001 PHE O 114 TYR 0.012 0.001 TYR K 66 ARG 0.002 0.000 ARG D 12 *********************** 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 : 2.654 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: F 31 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7840 (mppt) REVERT: H 53 PHE cc_start: 0.8166 (m-80) cc_final: 0.7945 (t80) REVERT: I 24 MET cc_start: 0.8333 (mmm) cc_final: 0.8126 (mmm) REVERT: L 115 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7221 (tp30) REVERT: M 64 LEU cc_start: 0.5138 (mt) cc_final: 0.4730 (tt) REVERT: N 12 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7819 (mttm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 3.7533 time to fit residues: 1459.6367 Evaluate side-chains 279 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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: 2.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 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: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 GLN I 15 GLN J 16 GLN O 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 25754 Z= 0.405 Angle : 0.783 16.441 37076 Z= 0.412 Chirality : 0.045 0.273 4511 Planarity : 0.007 0.137 2901 Dihedral : 22.063 178.085 9591 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.54 % Allowed : 11.08 % Favored : 87.38 % 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: 0.74 (0.20), residues: 1700 helix: 1.14 (0.21), residues: 583 sheet: 0.36 (0.29), residues: 311 loop : 0.21 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 133 HIS 0.004 0.001 HIS N 28 PHE 0.018 0.002 PHE K 15 TYR 0.016 0.002 TYR E 199 ARG 0.006 0.001 ARG L 25 *********************** 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 311 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 288 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8157 (tt) REVERT: D 148 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7010 (mm-40) REVERT: I 24 MET cc_start: 0.8400 (mmm) cc_final: 0.8173 (mmm) REVERT: M 64 LEU cc_start: 0.5168 (mt) cc_final: 0.4700 (tt) REVERT: N 12 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7875 (mttm) REVERT: N 37 MET cc_start: 0.8508 (mmm) cc_final: 0.8130 (mmm) REVERT: O 108 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8227 (m-30) outliers start: 23 outliers final: 14 residues processed: 299 average time/residue: 3.2205 time to fit residues: 1084.8631 Evaluate side-chains 291 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 275 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 108 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25754 Z= 0.192 Angle : 0.655 15.847 37076 Z= 0.355 Chirality : 0.038 0.224 4511 Planarity : 0.006 0.128 2901 Dihedral : 21.792 178.324 9591 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 12.48 % Favored : 85.91 % 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: 0.39 (0.29), residues: 323 loop : 0.34 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 179 HIS 0.002 0.001 HIS P 96 PHE 0.012 0.001 PHE K 15 TYR 0.013 0.001 TYR F 64 ARG 0.005 0.000 ARG L 25 *********************** 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 316 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 292 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 MET cc_start: 0.8359 (mmm) cc_final: 0.8127 (mmm) REVERT: J 8 GLU cc_start: 0.7650 (mp0) cc_final: 0.7448 (mp0) REVERT: M 64 LEU cc_start: 0.5153 (mt) cc_final: 0.4690 (tt) REVERT: N 12 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7848 (mttm) outliers start: 24 outliers final: 12 residues processed: 303 average time/residue: 3.2823 time to fit residues: 1119.7918 Evaluate side-chains 294 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 282 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain P residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8686 moved from start: 0.2002 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= 0.290 Angle : 0.706 16.063 37076 Z= 0.377 Chirality : 0.041 0.228 4511 Planarity : 0.006 0.133 2901 Dihedral : 21.845 178.653 9591 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.80 % Allowed : 13.48 % Favored : 84.71 % 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: 1.11 (0.20), residues: 1700 helix: 1.64 (0.21), residues: 584 sheet: 0.42 (0.29), residues: 321 loop : 0.31 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 82 HIS 0.003 0.001 HIS I 56 PHE 0.016 0.002 PHE K 15 TYR 0.017 0.001 TYR F 64 ARG 0.003 0.000 ARG L 25 *********************** 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 310 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 283 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 GLU cc_start: 0.8010 (tp30) cc_final: 0.7789 (tt0) REVERT: I 24 MET cc_start: 0.8373 (mmm) cc_final: 0.8138 (mmm) REVERT: I 37 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: M 64 LEU cc_start: 0.5219 (mt) cc_final: 0.4719 (tt) REVERT: N 12 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7884 (mttm) REVERT: O 108 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8212 (m-30) outliers start: 27 outliers final: 17 residues processed: 294 average time/residue: 3.2632 time to fit residues: 1078.2868 Evaluate side-chains 295 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 276 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 75 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2099 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= 0.193 Angle : 0.655 15.659 37076 Z= 0.355 Chirality : 0.038 0.240 4511 Planarity : 0.006 0.127 2901 Dihedral : 21.752 178.769 9591 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.47 % Allowed : 14.35 % Favored : 84.18 % 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: 1.28 (0.21), residues: 1700 helix: 1.86 (0.21), residues: 584 sheet: 0.45 (0.29), residues: 321 loop : 0.38 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 133 HIS 0.003 0.001 HIS K 22 PHE 0.013 0.001 PHE K 15 TYR 0.015 0.001 TYR F 64 ARG 0.003 0.000 ARG L 25 *********************** 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 304 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 GLU cc_start: 0.8001 (tp30) cc_final: 0.7801 (tt0) REVERT: I 24 MET cc_start: 0.8346 (mmm) cc_final: 0.8110 (mmm) REVERT: I 37 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: J 108 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7430 (ttp80) REVERT: M 64 LEU cc_start: 0.5164 (mt) cc_final: 0.4690 (tt) REVERT: N 12 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7855 (mttm) outliers start: 22 outliers final: 15 residues processed: 290 average time/residue: 3.3024 time to fit residues: 1079.6758 Evaluate side-chains 293 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 276 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain P residue 75 SER 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.8674 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25754 Z= 0.246 Angle : 0.680 15.925 37076 Z= 0.366 Chirality : 0.039 0.231 4511 Planarity : 0.006 0.130 2901 Dihedral : 21.775 178.892 9591 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.80 % Allowed : 14.62 % Favored : 83.58 % 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: 1.29 (0.20), residues: 1700 helix: 1.89 (0.21), residues: 583 sheet: 0.47 (0.29), residues: 321 loop : 0.35 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 133 HIS 0.003 0.001 HIS K 22 PHE 0.015 0.001 PHE K 15 TYR 0.016 0.001 TYR F 64 ARG 0.002 0.000 ARG J 130 *********************** 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 303 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 276 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 MET cc_start: 0.8350 (mmm) cc_final: 0.8101 (mmm) REVERT: I 37 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: J 108 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7428 (ttp80) REVERT: M 64 LEU cc_start: 0.5218 (mt) cc_final: 0.4705 (tt) REVERT: N 12 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7857 (mttm) REVERT: N 37 MET cc_start: 0.8499 (mmm) cc_final: 0.8231 (mmm) REVERT: O 108 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (m-30) outliers start: 27 outliers final: 17 residues processed: 288 average time/residue: 3.3125 time to fit residues: 1080.5137 Evaluate side-chains 294 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 274 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25754 Z= 0.307 Angle : 0.717 16.255 37076 Z= 0.381 Chirality : 0.041 0.226 4511 Planarity : 0.006 0.134 2901 Dihedral : 21.845 179.112 9591 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.60 % Allowed : 14.69 % Favored : 83.71 % 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: 1.22 (0.20), residues: 1700 helix: 1.82 (0.21), residues: 583 sheet: 0.48 (0.29), residues: 323 loop : 0.31 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 82 HIS 0.003 0.001 HIS I 56 PHE 0.017 0.002 PHE K 15 TYR 0.017 0.001 TYR F 64 ARG 0.006 0.000 ARG D 48 *********************** 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 301 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 277 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 MET cc_start: 0.8342 (mmm) cc_final: 0.8099 (mmm) REVERT: I 37 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: J 108 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7440 (ttp80) REVERT: M 64 LEU cc_start: 0.5218 (mt) cc_final: 0.4699 (tt) REVERT: N 12 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7874 (mttm) REVERT: O 108 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (m-30) outliers start: 24 outliers final: 17 residues processed: 288 average time/residue: 3.2890 time to fit residues: 1070.2263 Evaluate side-chains 295 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 75 SER 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: 1.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25754 Z= 0.269 Angle : 0.701 16.051 37076 Z= 0.375 Chirality : 0.040 0.229 4511 Planarity : 0.006 0.132 2901 Dihedral : 21.832 179.156 9591 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.78 % 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: 1.28 (0.20), residues: 1700 helix: 1.93 (0.21), residues: 577 sheet: 0.45 (0.29), residues: 326 loop : 0.33 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 133 HIS 0.003 0.001 HIS K 22 PHE 0.016 0.002 PHE K 15 TYR 0.016 0.001 TYR F 64 ARG 0.004 0.000 ARG D 48 *********************** 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 299 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 276 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (tt) REVERT: I 24 MET cc_start: 0.8337 (mmm) cc_final: 0.8109 (mmm) REVERT: I 37 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: J 108 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: M 64 LEU cc_start: 0.5213 (mt) cc_final: 0.4693 (tt) REVERT: N 12 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7734 (mmtm) REVERT: O 108 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (m-30) outliers start: 23 outliers final: 17 residues processed: 286 average time/residue: 3.3409 time to fit residues: 1075.2959 Evaluate side-chains 297 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25754 Z= 0.304 Angle : 0.716 16.251 37076 Z= 0.381 Chirality : 0.041 0.227 4511 Planarity : 0.006 0.133 2901 Dihedral : 21.844 179.324 9591 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.47 % Allowed : 14.49 % Favored : 84.05 % 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: 1.24 (0.20), residues: 1700 helix: 1.92 (0.21), residues: 577 sheet: 0.45 (0.29), residues: 326 loop : 0.28 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 133 HIS 0.004 0.001 HIS I 56 PHE 0.016 0.002 PHE K 15 TYR 0.017 0.001 TYR F 64 ARG 0.003 0.000 ARG J 130 *********************** 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 297 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 MET cc_start: 0.8347 (mmm) cc_final: 0.8092 (mmm) REVERT: I 37 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: J 108 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: M 64 LEU cc_start: 0.5218 (mt) cc_final: 0.4690 (tt) REVERT: N 12 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7749 (mmtm) REVERT: N 37 MET cc_start: 0.8499 (mmm) cc_final: 0.8292 (mmm) REVERT: O 108 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8270 (m-30) outliers start: 22 outliers final: 14 residues processed: 286 average time/residue: 3.3617 time to fit residues: 1082.4936 Evaluate side-chains 289 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 272 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 198 optimal weight: 0.0270 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 P 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25754 Z= 0.168 Angle : 0.646 15.527 37076 Z= 0.350 Chirality : 0.037 0.238 4511 Planarity : 0.006 0.125 2901 Dihedral : 21.698 179.185 9591 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.13 % Allowed : 15.02 % Favored : 83.85 % 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: 1.43 (0.21), residues: 1700 helix: 2.14 (0.22), residues: 583 sheet: 0.46 (0.28), residues: 327 loop : 0.37 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 133 HIS 0.002 0.001 HIS P 96 PHE 0.011 0.001 PHE K 15 TYR 0.013 0.001 TYR F 64 ARG 0.003 0.000 ARG D 48 ********************** 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 301 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 284 time to evaluate : 2.991 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: I 24 MET cc_start: 0.8309 (mmm) cc_final: 0.8069 (mmm) REVERT: J 108 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7445 (ttp80) REVERT: M 64 LEU cc_start: 0.5235 (mt) cc_final: 0.4728 (tt) REVERT: N 12 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7715 (mmtm) outliers start: 17 outliers final: 12 residues processed: 290 average time/residue: 3.2389 time to fit residues: 1059.7587 Evaluate side-chains 292 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 279 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain O residue 180 ASN Chi-restraints excluded: chain P residue 75 SER 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: 0.8980 chunk 158 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 GLN O 164 GLN O 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.089845 restraints weight = 63224.206| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.00 r_work: 0.2750 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 25754 Z= 0.192 Angle : 0.754 59.160 37076 Z= 0.433 Chirality : 0.037 0.238 4511 Planarity : 0.006 0.125 2901 Dihedral : 21.701 179.179 9591 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.07 % Allowed : 15.15 % Favored : 83.78 % 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: 1.44 (0.21), residues: 1700 helix: 2.15 (0.22), residues: 583 sheet: 0.47 (0.28), residues: 327 loop : 0.37 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 179 HIS 0.002 0.001 HIS P 96 PHE 0.011 0.001 PHE K 15 TYR 0.014 0.001 TYR F 64 ARG 0.007 0.000 ARG G 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19781.10 seconds wall clock time: 349 minutes 34.31 seconds (20974.31 seconds total)