Starting phenix.real_space_refine on Thu Dec 7 16:25:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4u_23666/12_2023/7m4u_23666_updated.pdb" } resolution = 2.71 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= 0.004 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1197 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 1527 5.49 5 Mg 83 5.21 5 S 62 5.16 5 C 26320 2.51 5 N 9589 2.21 5 O 14182 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "p PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 51764 Number of models: 1 Model: "" Number of chains: 27 Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 105, 'rna2p_pyr': 96, 'rna3p': 8, 'rna3p_pur': 758, 'rna3p_pyr': 560} Link IDs: {'rna2p': 201, 'rna3p': 1326} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1111 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 693 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "q" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "a" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 122 Unusual residues: {' MG': 82, 'YQM': 1} Classifications: {'undetermined': 83} Link IDs: {None: 82} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "i" 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: "t" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 20.50, per 1000 atoms: 0.40 Number of scatterers: 51764 At special positions: 0 Unit cell: (144.16, 200.976, 256.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 P 1527 15.00 Mg 83 11.99 F 1 9.00 O 14182 8.00 N 9589 7.00 C 26320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.59 Conformation dependent library (CDL) restraints added in 3.1 seconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 20 sheets defined 40.3% alpha, 16.2% beta 470 base pairs and 764 stacking pairs defined. Time for finding SS restraints: 21.99 Creating SS restraints... Processing helix chain 'b' and resid 9 through 14 Processing helix chain 'b' and resid 22 through 24 No H-bonds generated for 'chain 'b' and resid 22 through 24' Processing helix chain 'b' and resid 46 through 65 Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 76 through 89 removed outlier: 4.751A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 124 removed outlier: 3.677A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 128 No H-bonds generated for 'chain 'b' and resid 126 through 128' Processing helix chain 'b' and resid 133 through 150 Processing helix chain 'b' and resid 172 through 181 Processing helix chain 'b' and resid 209 through 226 Processing helix chain 'c' and resid 9 through 11 No H-bonds generated for 'chain 'c' and resid 9 through 11' Processing helix chain 'c' and resid 29 through 46 Processing helix chain 'c' and resid 73 through 77 Processing helix chain 'c' and resid 82 through 94 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 113 through 125 Processing helix chain 'c' and resid 130 through 143 Processing helix chain 'c' and resid 157 through 159 No H-bonds generated for 'chain 'c' and resid 157 through 159' Processing helix chain 'c' and resid 210 through 214 removed outlier: 4.183A pdb=" N VAL c 214 " --> pdb=" O GLY c 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 210 through 214' Processing helix chain 'd' and resid 9 through 15 Processing helix chain 'd' and resid 28 through 32 Processing helix chain 'd' and resid 52 through 67 removed outlier: 3.788A pdb=" N TYR d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 83 Processing helix chain 'd' and resid 88 through 97 Processing helix chain 'd' and resid 100 through 106 Processing helix chain 'd' and resid 113 through 121 Processing helix chain 'd' and resid 155 through 166 removed outlier: 3.642A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 207 Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.638A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 144 Processing helix chain 'e' and resid 149 through 156 Processing helix chain 'e' and resid 160 through 163 No H-bonds generated for 'chain 'e' and resid 160 through 163' Processing helix chain 'f' and resid 13 through 32 removed outlier: 4.523A pdb=" N ASP f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL f 19 " --> pdb=" O ASP f 16 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL f 22 " --> pdb=" O VAL f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 80 Processing helix chain 'g' and resid 21 through 30 Processing helix chain 'g' and resid 36 through 53 removed outlier: 3.698A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 69 Processing helix chain 'g' and resid 93 through 110 removed outlier: 3.568A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 129 removed outlier: 3.674A pdb=" N ALA g 128 " --> pdb=" O LEU g 124 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 138 Processing helix chain 'h' and resid 6 through 19 Processing helix chain 'h' and resid 31 through 43 Processing helix chain 'h' and resid 90 through 92 No H-bonds generated for 'chain 'h' and resid 90 through 92' Processing helix chain 'h' and resid 114 through 120 Processing helix chain 'i' and resid 33 through 36 No H-bonds generated for 'chain 'i' and resid 33 through 36' Processing helix chain 'i' and resid 40 through 52 Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 70 through 88 Processing helix chain 'i' and resid 90 through 98 Proline residue: i 94 - end of helix Processing helix chain 'j' and resid 15 through 32 Processing helix chain 'j' and resid 81 through 88 removed outlier: 4.164A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 57 Processing helix chain 'k' and resid 59 through 76 removed outlier: 4.047A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 101 removed outlier: 3.718A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'm' and resid 15 through 21 removed outlier: 4.793A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 37 Processing helix chain 'm' and resid 45 through 47 No H-bonds generated for 'chain 'm' and resid 45 through 47' Processing helix chain 'm' and resid 50 through 61 Processing helix chain 'm' and resid 67 through 83 Processing helix chain 'm' and resid 86 through 93 Processing helix chain 'm' and resid 107 through 110 No H-bonds generated for 'chain 'm' and resid 107 through 110' Processing helix chain 'n' and resid 4 through 19 Processing helix chain 'n' and resid 21 through 31 Processing helix chain 'n' and resid 38 through 50 Processing helix chain 'n' and resid 53 through 55 No H-bonds generated for 'chain 'n' and resid 53 through 55' Processing helix chain 'n' and resid 57 through 59 No H-bonds generated for 'chain 'n' and resid 57 through 59' Processing helix chain 'n' and resid 81 through 90 removed outlier: 3.536A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 15 Processing helix chain 'o' and resid 25 through 45 removed outlier: 3.617A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 73 removed outlier: 3.811A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 85 Processing helix chain 'p' and resid 72 through 80 Processing helix chain 'p' and resid 87 through 100 Processing helix chain 'r' and resid 26 through 30 Processing helix chain 'r' and resid 42 through 45 No H-bonds generated for 'chain 'r' and resid 42 through 45' Processing helix chain 'r' and resid 49 through 64 Processing helix chain 's' and resid 5 through 7 No H-bonds generated for 'chain 's' and resid 5 through 7' Processing helix chain 's' and resid 13 through 24 Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 64 through 66 No H-bonds generated for 'chain 's' and resid 64 through 66' Processing helix chain 's' and resid 71 through 74 Processing helix chain 't' and resid 5 through 41 removed outlier: 3.687A pdb=" N VAL t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 63 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 69 through 86 removed outlier: 3.791A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 26 Processing helix chain 'u' and resid 28 through 36 removed outlier: 3.736A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 41 through 63 Processing sheet with id= A, first strand: chain 'b' and resid 69 through 72 removed outlier: 6.972A pdb=" N ALA b 162 " --> pdb=" O LEU b 70 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL b 72 " --> pdb=" O ALA b 162 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE b 164 " --> pdb=" O VAL b 72 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL b 165 " --> pdb=" O PRO b 184 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE b 186 " --> pdb=" O VAL b 165 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR b 200 " --> pdb=" O GLY b 187 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL b 189 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE b 202 " --> pdb=" O VAL b 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'c' and resid 55 through 58 Processing sheet with id= C, first strand: chain 'c' and resid 164 through 171 removed outlier: 6.619A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'd' and resid 125 through 127 Processing sheet with id= E, first strand: chain 'e' and resid 45 through 52 removed outlier: 6.991A pdb=" N VAL e 37 " --> pdb=" O LEU e 14 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU e 14 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLY e 39 " --> pdb=" O GLU e 12 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU e 12 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'e' and resid 84 through 88 Processing sheet with id= G, first strand: chain 'f' and resid 87 through 92 removed outlier: 3.935A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR f 59 " --> pdb=" O GLY f 43 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'f' and resid 36 through 41 removed outlier: 6.467A pdb=" N ASN f 63 " --> pdb=" O HIS f 37 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU f 39 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU f 61 " --> pdb=" O LEU f 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'g' and resid 74 through 76 Processing sheet with id= J, first strand: chain 'h' and resid 24 through 28 Processing sheet with id= K, first strand: chain 'h' and resid 76 through 78 removed outlier: 6.731A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE h 129 " --> pdb=" O ILE h 102 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE h 102 " --> pdb=" O PHE h 129 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'i' and resid 4 through 10 Processing sheet with id= M, first strand: chain 'j' and resid 96 through 101 Processing sheet with id= N, first strand: chain 'j' and resid 45 through 52 Processing sheet with id= O, first strand: chain 'k' and resid 40 through 45 removed outlier: 7.084A pdb=" N ILE k 33 " --> pdb=" O LEU k 41 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP k 43 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL k 31 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR k 45 " --> pdb=" O THR k 29 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR k 29 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN k 80 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA k 20 " --> pdb=" O ASN k 80 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP k 82 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE k 22 " --> pdb=" O ASP k 82 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU k 84 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA k 24 " --> pdb=" O LEU k 84 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS k 86 " --> pdb=" O ALA k 24 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS k 105 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL k 83 " --> pdb=" O LYS k 105 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN k 107 " --> pdb=" O VAL k 83 " (cutoff:3.500A) removed outlier: 12.540A pdb=" N VAL k 85 " --> pdb=" O ASN k 107 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ILE k 109 " --> pdb=" O VAL k 85 " (cutoff:3.500A) removed outlier: 12.271A pdb=" N GLY k 87 " --> pdb=" O ILE k 109 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP k 111 " --> pdb=" O GLY k 87 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'l' and resid 95 through 97 removed outlier: 6.641A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'p' and resid 20 through 29 removed outlier: 3.721A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL p 39 " --> pdb=" O ARG p 53 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ARG p 53 " --> pdb=" O VAL p 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'q' and resid 74 through 76 removed outlier: 16.983A pdb=" N THR q 8 " --> pdb=" O ARG q 29 " (cutoff:3.500A) removed outlier: 13.364A pdb=" N ARG q 29 " --> pdb=" O THR q 8 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR q 10 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU q 27 " --> pdb=" O THR q 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL q 23 " --> pdb=" O VAL q 14 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'q' and resid 59 through 61 removed outlier: 6.824A pdb=" N THR q 61 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL q 79 " --> pdb=" O THR q 61 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 's' and resid 31 through 33 808 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1188 hydrogen bonds 1878 hydrogen bond angles 0 basepair planarities 470 basepair parallelities 764 stacking parallelities Total time for adding SS restraints: 43.38 Time building geometry restraints manager: 22.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5161 1.31 - 1.43: 23933 1.43 - 1.56: 23411 1.56 - 1.69: 3062 1.69 - 1.81: 112 Bond restraints: 55679 Sorted by residual: bond pdb=" C14 YQM a1601 " pdb=" C15 YQM a1601 " ideal model delta sigma weight residual 1.038 1.552 -0.514 2.00e-02 2.50e+03 6.62e+02 bond pdb=" C08 YQM a1601 " pdb=" C09 YQM a1601 " ideal model delta sigma weight residual 1.948 1.550 0.398 2.00e-02 2.50e+03 3.95e+02 bond pdb=" C15 YQM a1601 " pdb=" C16 YQM a1601 " ideal model delta sigma weight residual 1.737 1.410 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C07 YQM a1601 " pdb=" C16 YQM a1601 " ideal model delta sigma weight residual 1.205 1.531 -0.326 2.00e-02 2.50e+03 2.65e+02 bond pdb=" C06 YQM a1601 " pdb=" C07 YQM a1601 " ideal model delta sigma weight residual 1.872 1.568 0.304 2.00e-02 2.50e+03 2.30e+02 ... (remaining 55674 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.91: 9452 106.91 - 114.55: 35344 114.55 - 122.20: 26812 122.20 - 129.84: 10225 129.84 - 137.49: 929 Bond angle restraints: 82762 Sorted by residual: angle pdb=" C ASN d 128 " pdb=" CA ASN d 128 " pdb=" CB ASN d 128 " ideal model delta sigma weight residual 111.80 124.83 -13.03 1.46e+00 4.69e-01 7.97e+01 angle pdb=" C ARG d 131 " pdb=" CA ARG d 131 " pdb=" CB ARG d 131 " ideal model delta sigma weight residual 110.29 124.80 -14.51 1.64e+00 3.72e-01 7.83e+01 angle pdb=" C1' 2MG a 963 " pdb=" N9 2MG a 963 " pdb=" C8 2MG a 963 " ideal model delta sigma weight residual 110.07 128.30 -18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 127.09 -17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C13 YQM a1601 " pdb=" C14 YQM a1601 " pdb=" C15 YQM a1601 " ideal model delta sigma weight residual 109.00 124.39 -15.39 3.00e+00 1.11e-01 2.63e+01 ... (remaining 82757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 31031 36.00 - 71.99: 2889 71.99 - 107.99: 369 107.99 - 143.98: 8 143.98 - 179.98: 26 Dihedral angle restraints: 34323 sinusoidal: 27480 harmonic: 6843 Sorted by residual: dihedral pdb=" C ASN d 128 " pdb=" N ASN d 128 " pdb=" CA ASN d 128 " pdb=" CB ASN d 128 " ideal model delta harmonic sigma weight residual -122.60 -149.52 26.92 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" C ARG d 131 " pdb=" N ARG d 131 " pdb=" CA ARG d 131 " pdb=" CB ARG d 131 " ideal model delta harmonic sigma weight residual -122.60 -146.57 23.97 0 2.50e+00 1.60e-01 9.19e+01 dihedral pdb=" N ASN d 128 " pdb=" C ASN d 128 " pdb=" CA ASN d 128 " pdb=" CB ASN d 128 " ideal model delta harmonic sigma weight residual 122.80 145.91 -23.11 0 2.50e+00 1.60e-01 8.55e+01 ... (remaining 34320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 10459 0.210 - 0.420: 5 0.420 - 0.631: 0 0.631 - 0.841: 0 0.841 - 1.051: 2 Chirality restraints: 10466 Sorted by residual: chirality pdb=" CA ASN d 128 " pdb=" N ASN d 128 " pdb=" C ASN d 128 " pdb=" CB ASN d 128 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.76e+01 chirality pdb=" CA ARG d 131 " pdb=" N ARG d 131 " pdb=" C ARG d 131 " pdb=" CB ARG d 131 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" C1* PSU a 513 " pdb=" O4* PSU a 513 " pdb=" C2* PSU a 513 " pdb=" C5 PSU a 513 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 10463 not shown) Planarity restraints: 4834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " -0.042 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' 7MG a 524 " -0.467 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " -0.783 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " 0.596 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " 0.229 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " -0.903 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " -0.184 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " 0.969 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' MA6 a1516 " -0.058 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' MA6 a1516 " -0.454 2.00e-02 2.50e+03 pdb=" O4' MA6 a1516 " -0.677 2.00e-02 2.50e+03 pdb=" C3' MA6 a1516 " 0.592 2.00e-02 2.50e+03 pdb=" O3' MA6 a1516 " 0.632 2.00e-02 2.50e+03 pdb=" C2' MA6 a1516 " 0.189 2.00e-02 2.50e+03 pdb=" O2' MA6 a1516 " -0.950 2.00e-02 2.50e+03 pdb=" C1' MA6 a1516 " -0.213 2.00e-02 2.50e+03 pdb=" N9 MA6 a1516 " 0.939 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4OC a1399 " -0.050 2.00e-02 2.50e+03 5.87e-01 7.76e+03 pdb=" C4' 4OC a1399 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 4OC a1399 " -0.634 2.00e-02 2.50e+03 pdb=" C3' 4OC a1399 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 4OC a1399 " 0.608 2.00e-02 2.50e+03 pdb=" C2' 4OC a1399 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 4OC a1399 " -0.943 2.00e-02 2.50e+03 pdb=" C1' 4OC a1399 " -0.228 2.00e-02 2.50e+03 pdb=" N1 4OC a1399 " 0.897 2.00e-02 2.50e+03 ... (remaining 4831 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 276 2.40 - 3.02: 27493 3.02 - 3.65: 89019 3.65 - 4.27: 145672 4.27 - 4.90: 196359 Nonbonded interactions: 458819 Sorted by model distance: nonbonded pdb="MG MG a1613 " pdb=" O HOH a1720 " model vdw 1.771 2.170 nonbonded pdb="MG MG a1632 " pdb=" O HOH t 101 " model vdw 1.775 2.170 nonbonded pdb="MG MG a1646 " pdb=" O HOH a1764 " model vdw 1.787 2.170 nonbonded pdb="MG MG a1639 " pdb=" O HOH a1707 " model vdw 1.794 2.170 nonbonded pdb="MG MG a1617 " pdb=" O HOH a1842 " model vdw 1.801 2.170 ... (remaining 458814 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=1.00 max=1.00 mean=1.00 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.050 Extract box with map and model: 26.190 Check model and map are aligned: 0.710 Set scattering table: 0.380 Process input model: 143.160 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:10.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.006 0.514 55679 Z= 0.312 Angle : 0.581 18.228 82762 Z= 0.310 Chirality : 0.037 1.051 10466 Planarity : 0.024 0.612 4834 Dihedral : 21.770 179.979 29907 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.68 % Rotamer: Outliers : 0.20 % Allowed : 0.15 % Favored : 99.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2346 helix: 2.05 (0.17), residues: 996 sheet: 1.06 (0.26), residues: 378 loop : -0.88 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 25 HIS 0.006 0.001 HIS b 41 PHE 0.016 0.001 PHE s 44 TYR 0.013 0.001 TYR i 5 ARG 0.006 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 473 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 476 average time/residue: 1.7468 time to fit residues: 998.3207 Evaluate side-chains 413 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 0.5980 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 40.0000 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 chunk 347 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 GLN b 91 GLN c 28 GLN d 73 GLN d 91 ASN ** d 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS j 56 HIS j 99 GLN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 32 ASN n 49 GLN o 37 ASN o 40 GLN o 62 GLN p 84 GLN r 54 GLN t 3 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 55679 Z= 0.298 Angle : 0.776 14.919 82762 Z= 0.413 Chirality : 0.042 0.362 10466 Planarity : 0.008 0.132 4834 Dihedral : 22.440 179.830 25233 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 3.23 % Allowed : 11.57 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2346 helix: 1.83 (0.16), residues: 1004 sheet: 0.93 (0.26), residues: 367 loop : -0.88 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 25 HIS 0.009 0.001 HIS j 15 PHE 0.021 0.002 PHE s 44 TYR 0.017 0.002 TYR n 73 ARG 0.008 0.001 ARG g 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 420 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 28 residues processed: 442 average time/residue: 1.7353 time to fit residues: 922.3113 Evaluate side-chains 445 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 417 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 9 residues processed: 19 average time/residue: 0.5734 time to fit residues: 20.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 289 optimal weight: 30.0000 chunk 236 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 279 optimal weight: 0.0020 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 ASN c 28 GLN c 123 GLN d 42 HIS d 73 GLN j 99 GLN l 29 GLN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN n 49 GLN o 40 GLN o 62 GLN p 84 GLN r 54 GLN t 3 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55679 Z= 0.225 Angle : 0.703 14.056 82762 Z= 0.382 Chirality : 0.038 0.348 10466 Planarity : 0.007 0.128 4834 Dihedral : 22.305 179.886 25233 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 14.03 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2346 helix: 1.90 (0.16), residues: 1004 sheet: 0.93 (0.26), residues: 382 loop : -0.86 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.007 0.001 HIS j 15 PHE 0.014 0.002 PHE s 10 TYR 0.015 0.002 TYR i 5 ARG 0.006 0.001 ARG g 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 415 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 441 average time/residue: 1.7511 time to fit residues: 930.0340 Evaluate side-chains 440 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 407 time to evaluate : 2.447 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 13 residues processed: 20 average time/residue: 0.3898 time to fit residues: 17.4581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 4.9990 chunk 261 optimal weight: 0.0770 chunk 180 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 331 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN d 73 GLN g 28 ASN g 54 ASN j 99 GLN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN n 49 GLN o 40 GLN o 62 GLN p 84 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 55679 Z= 0.226 Angle : 0.706 14.181 82762 Z= 0.384 Chirality : 0.038 0.353 10466 Planarity : 0.007 0.127 4834 Dihedral : 22.270 179.996 25233 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.38 % Rotamer: Outliers : 3.84 % Allowed : 16.13 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2346 helix: 1.87 (0.16), residues: 1007 sheet: 0.91 (0.26), residues: 383 loop : -0.89 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.006 0.001 HIS j 15 PHE 0.015 0.002 PHE s 44 TYR 0.016 0.002 TYR i 5 ARG 0.007 0.001 ARG g 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 416 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 39 residues processed: 453 average time/residue: 1.7408 time to fit residues: 950.9541 Evaluate side-chains 453 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 414 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 17 residues processed: 22 average time/residue: 0.4993 time to fit residues: 21.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 0.9990 chunk 210 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 315 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 61 GLN c 28 GLN c 123 GLN d 73 GLN j 99 GLN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS l 111 ASN m 52 GLN n 49 GLN o 40 GLN o 62 GLN p 84 GLN r 54 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55679 Z= 0.196 Angle : 0.681 14.135 82762 Z= 0.372 Chirality : 0.037 0.344 10466 Planarity : 0.007 0.126 4834 Dihedral : 22.223 179.945 25233 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.98 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 17.61 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2346 helix: 1.95 (0.16), residues: 1006 sheet: 0.94 (0.26), residues: 383 loop : -0.89 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.006 0.001 HIS j 15 PHE 0.014 0.002 PHE s 10 TYR 0.014 0.002 TYR i 5 ARG 0.009 0.001 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 412 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 447 average time/residue: 1.7513 time to fit residues: 957.0874 Evaluate side-chains 441 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 402 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 22 residues processed: 17 average time/residue: 0.5040 time to fit residues: 17.6126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 370 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 61 GLN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 123 GLN d 73 GLN j 99 GLN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 62 GLN p 84 GLN r 54 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 55679 Z= 0.510 Angle : 0.961 14.494 82762 Z= 0.490 Chirality : 0.051 0.436 10466 Planarity : 0.009 0.137 4834 Dihedral : 22.548 179.218 25233 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.67 % Favored : 96.04 % Rotamer: Outliers : 4.51 % Allowed : 17.67 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2346 helix: 1.34 (0.16), residues: 1000 sheet: 0.71 (0.26), residues: 370 loop : -1.20 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP c 201 HIS 0.012 0.002 HIS s 14 PHE 0.026 0.003 PHE s 10 TYR 0.022 0.003 TYR d 78 ARG 0.013 0.001 ARG n 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 403 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 51 residues processed: 449 average time/residue: 1.6953 time to fit residues: 921.8578 Evaluate side-chains 452 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 401 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 27 residues processed: 24 average time/residue: 0.6256 time to fit residues: 26.0033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 0.0270 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 0.0870 chunk 270 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 369 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 61 GLN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN d 73 GLN j 99 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 32 ASN n 49 GLN o 40 GLN o 62 GLN p 84 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 55679 Z= 0.137 Angle : 0.654 14.459 82762 Z= 0.361 Chirality : 0.035 0.368 10466 Planarity : 0.006 0.123 4834 Dihedral : 22.212 179.561 25233 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.77 % Favored : 96.93 % Rotamer: Outliers : 2.46 % Allowed : 20.07 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2346 helix: 1.90 (0.16), residues: 1005 sheet: 0.98 (0.26), residues: 379 loop : -0.90 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 201 HIS 0.005 0.001 HIS c 18 PHE 0.010 0.001 PHE e 140 TYR 0.009 0.001 TYR c 23 ARG 0.008 0.000 ARG l 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 415 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 451 average time/residue: 1.6726 time to fit residues: 918.3157 Evaluate side-chains 435 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 403 time to evaluate : 2.367 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.6886 time to fit residues: 10.9837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 0.4980 chunk 147 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 251 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 61 GLN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 123 GLN d 73 GLN g 28 ASN j 99 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN n 49 GLN o 40 GLN o 62 GLN p 84 GLN r 54 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 55679 Z= 0.342 Angle : 0.807 14.646 82762 Z= 0.425 Chirality : 0.043 0.395 10466 Planarity : 0.008 0.131 4834 Dihedral : 22.342 179.871 25233 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 2.87 % Allowed : 20.23 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2346 helix: 1.62 (0.16), residues: 1004 sheet: 0.84 (0.26), residues: 375 loop : -1.06 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 201 HIS 0.008 0.001 HIS j 15 PHE 0.024 0.002 PHE o 43 TYR 0.018 0.002 TYR n 73 ARG 0.008 0.001 ARG n 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 402 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 43 residues processed: 433 average time/residue: 1.6738 time to fit residues: 879.2492 Evaluate side-chains 445 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 402 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 25 residues processed: 18 average time/residue: 0.6569 time to fit residues: 20.7149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 322 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 270 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 342 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 61 GLN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 123 GLN d 73 GLN h 18 GLN j 99 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 32 ASN n 49 GLN o 40 GLN o 62 GLN p 84 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 55679 Z= 0.159 Angle : 0.662 14.182 82762 Z= 0.364 Chirality : 0.036 0.352 10466 Planarity : 0.007 0.124 4834 Dihedral : 22.191 179.829 25233 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.90 % Favored : 96.80 % Rotamer: Outliers : 2.15 % Allowed : 21.15 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2346 helix: 1.88 (0.17), residues: 1005 sheet: 0.94 (0.27), residues: 374 loop : -0.90 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 201 HIS 0.004 0.001 HIS c 18 PHE 0.016 0.001 PHE o 43 TYR 0.012 0.001 TYR i 5 ARG 0.007 0.001 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 406 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 436 average time/residue: 1.6879 time to fit residues: 892.0379 Evaluate side-chains 427 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 395 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.4129 time to fit residues: 7.8903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 252 optimal weight: 0.4980 chunk 381 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 123 GLN d 73 GLN j 99 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 62 GLN p 84 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55679 Z= 0.211 Angle : 0.698 13.999 82762 Z= 0.379 Chirality : 0.037 0.357 10466 Planarity : 0.007 0.126 4834 Dihedral : 22.199 179.688 25233 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 1.79 % Allowed : 21.81 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2346 helix: 1.85 (0.16), residues: 999 sheet: 0.92 (0.27), residues: 374 loop : -0.93 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 201 HIS 0.006 0.001 HIS j 15 PHE 0.021 0.002 PHE o 43 TYR 0.015 0.002 TYR i 5 ARG 0.009 0.001 ARG m 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 397 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 424 average time/residue: 1.7049 time to fit residues: 875.7933 Evaluate side-chains 424 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 393 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 5 average time/residue: 0.4236 time to fit residues: 6.4983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 1.9990 chunk 323 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 304 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 312 optimal weight: 0.0270 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 123 GLN d 73 GLN j 99 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN o 40 GLN o 62 GLN p 84 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118691 restraints weight = 64835.584| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.81 r_work: 0.3028 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55679 Z= 0.191 Angle : 0.684 13.891 82762 Z= 0.374 Chirality : 0.037 0.351 10466 Planarity : 0.007 0.126 4834 Dihedral : 22.193 179.884 25233 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.24 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 22.12 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2346 helix: 1.85 (0.16), residues: 999 sheet: 0.94 (0.27), residues: 374 loop : -0.91 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 201 HIS 0.005 0.001 HIS j 15 PHE 0.017 0.001 PHE o 43 TYR 0.014 0.002 TYR i 5 ARG 0.008 0.001 ARG c 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14118.61 seconds wall clock time: 247 minutes 17.08 seconds (14837.08 seconds total)