Starting phenix.real_space_refine (version: dev) on Sat Dec 17 02:37:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2022/7f0d_31398_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "1 GLU 37": "OE1" <-> "OE2" Residue "3 GLU 34": "OE1" <-> "OE2" Residue "6 GLU 36": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "P ASP 5": "OD1" <-> "OD2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S GLU 118": "OE1" <-> "OE2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 94": "OD1" <-> "OD2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V ASP 68": "OD1" <-> "OD2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 94362 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "A" Number of atoms: 66978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 300, 'rna2p_pyr': 164, 'rna3p_pur': 1483, 'rna3p_pyr': 1171} Link IDs: {'rna2p': 464, 'rna3p': 2653} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 299, 'rna2p_pyr': 164, 'rna3p_pur': 1484, 'rna3p_pyr': 1171} Link IDs: {'rna2p': 463, 'rna3p': 2654} Chain breaks: 1 bond proxies already assigned to first conformer: 74947 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1335 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1060 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 1, 'CTY': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A A2300 " occ=0.30 ... (42 atoms not shown) pdb=" C4 B A A2300 " occ=0.70 Time building chain proxies: 61.56, per 1000 atoms: 0.65 Number of scatterers: 94362 At special positions: 0 Unit cell: (206.96, 211.12, 237.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 3234 15.00 Mg 1 11.99 O 26888 8.00 N 17748 7.00 C 46439 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: 39.82 Conformation dependent library (CDL) restraints added in 3.3 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 39 sheets defined 20.6% alpha, 10.5% beta 982 base pairs and 1545 stacking pairs defined. Time for finding SS restraints: 44.65 Creating SS restraints... Processing helix chain '0' and resid 10 through 17 Processing helix chain '0' and resid 44 through 49 Processing helix chain '2' and resid 12 through 19 Processing helix chain '2' and resid 21 through 26 removed outlier: 4.023A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 39 Processing helix chain '3' and resid 8 through 11 No H-bonds generated for 'chain '3' and resid 8 through 11' Processing helix chain '3' and resid 39 through 42 No H-bonds generated for 'chain '3' and resid 39 through 42' Processing helix chain '3' and resid 52 through 61 removed outlier: 6.477A pdb=" N LYS 3 56 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG 3 57 " --> pdb=" O ASP 3 54 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR 3 59 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 110 through 127 Processing helix chain 'E' and resid 144 through 154 Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'F' and resid 13 through 25 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'F' and resid 100 through 109 removed outlier: 5.058A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 66 through 69 No H-bonds generated for 'chain 'J' and resid 66 through 69' Processing helix chain 'J' and resid 89 through 108 Proline residue: J 97 - end of helix Processing helix chain 'J' and resid 113 through 121 removed outlier: 4.576A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 94 through 100 Processing helix chain 'L' and resid 130 through 138 Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 112 through 124 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 46 - end of helix Processing helix chain 'N' and resid 60 through 66 Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.803A pdb=" N PHE N 87 " --> pdb=" O ILE N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 87' Processing helix chain 'O' and resid 10 through 22 removed outlier: 4.038A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 89 removed outlier: 4.311A pdb=" N VAL O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 117 Processing helix chain 'P' and resid 2 through 11 Proline residue: P 10 - end of helix Processing helix chain 'Q' and resid 7 through 19 removed outlier: 4.241A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 72 removed outlier: 3.668A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'Q' and resid 103 through 116 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'S' and resid 24 through 33 removed outlier: 4.042A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 46 Processing helix chain 'S' and resid 54 through 72 Processing helix chain 'S' and resid 76 through 78 No H-bonds generated for 'chain 'S' and resid 76 through 78' Processing helix chain 'T' and resid 7 through 9 No H-bonds generated for 'chain 'T' and resid 7 through 9' Processing helix chain 'T' and resid 19 through 27 removed outlier: 3.503A pdb=" N LEU T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 49 Processing helix chain 'U' and resid 89 through 91 No H-bonds generated for 'chain 'U' and resid 89 through 91' Processing helix chain 'V' and resid 19 through 27 Processing helix chain 'Y' and resid 9 through 12 No H-bonds generated for 'chain 'Y' and resid 9 through 12' Processing helix chain 'Y' and resid 16 through 37 Processing helix chain 'Y' and resid 46 through 65 Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 42 through 49 Processing sheet with id= A, first strand: chain '1' and resid 10 through 13 Processing sheet with id= B, first strand: chain '3' and resid 23 through 25 Processing sheet with id= C, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.387A pdb=" N LEU C 37 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG C 60 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 92 through 96 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 176 Processing sheet with id= F, first strand: chain 'D' and resid 192 through 194 removed outlier: 3.692A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS D 30 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS D 10 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 49 through 54 removed outlier: 3.549A pdb=" N TYR D 54 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 207 through 210 Processing sheet with id= I, first strand: chain 'E' and resid 181 through 184 removed outlier: 6.610A pdb=" N VAL E 160 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU E 184 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 162 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP E 199 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 163 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 201 " --> pdb=" O VAL E 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 43 through 45 removed outlier: 3.633A pdb=" N VAL F 96 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 45 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.820A pdb=" N VAL F 164 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 42 through 45 Processing sheet with id= M, first strand: chain 'G' and resid 84 through 88 removed outlier: 3.792A pdb=" N TYR G 84 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS G 131 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR G 133 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL G 126 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER G 135 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE G 124 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 104 through 106 removed outlier: 4.320A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.501A pdb=" N PHE J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE J 18 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE J 55 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 38 through 41 removed outlier: 6.277A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 18 through 20 removed outlier: 3.609A pdb=" N ASP K 45 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU K 20 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL K 43 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 75 through 77 Processing sheet with id= S, first strand: chain 'M' and resid 40 through 43 removed outlier: 6.284A pdb=" N LEU M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP M 93 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 33 through 35 removed outlier: 3.930A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= V, first strand: chain 'O' and resid 33 through 36 Processing sheet with id= W, first strand: chain 'P' and resid 39 through 45 removed outlier: 6.097A pdb=" N ASN P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL P 85 " --> pdb=" O ASN P 26 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE P 83 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 57 through 63 Processing sheet with id= Y, first strand: chain 'R' and resid 6 through 10 Processing sheet with id= Z, first strand: chain 'R' and resid 23 through 25 Processing sheet with id= AA, first strand: chain 'R' and resid 35 through 39 Processing sheet with id= AB, first strand: chain 'R' and resid 76 through 79 Processing sheet with id= AC, first strand: chain 'S' and resid 94 through 97 Processing sheet with id= AD, first strand: chain 'S' and resid 14 through 20 removed outlier: 5.853A pdb=" N SER S 111 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU S 118 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL S 81 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.606A pdb=" N LEU T 32 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR T 30 " --> pdb=" O PRO T 14 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 20 through 22 Processing sheet with id= AG, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.776A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 30 through 33 Processing sheet with id= AI, first strand: chain 'V' and resid 64 through 66 removed outlier: 6.576A pdb=" N ASP V 94 " --> pdb=" O LYS V 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 104 through 108 removed outlier: 4.399A pdb=" N VAL V 104 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 120 through 124 removed outlier: 3.708A pdb=" N THR V 123 " --> pdb=" O ASN V 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN V 178 " --> pdb=" O THR V 123 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'X' and resid 34 through 36 Processing sheet with id= AM, first strand: chain 'Z' and resid 34 through 37 560 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2554 hydrogen bonds 4238 hydrogen bond angles 0 basepair planarities 982 basepair parallelities 1545 stacking parallelities Total time for adding SS restraints: 148.19 Time building geometry restraints manager: 43.04 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: 8979 1.31 - 1.44: 46782 1.44 - 1.56: 40724 1.56 - 1.69: 6468 1.69 - 1.82: 86 Bond restraints: 103039 Sorted by residual: bond pdb=" C26 CTY A3201 " pdb=" C27 CTY A3201 " ideal model delta sigma weight residual 1.493 1.395 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C18 CTY A3201 " pdb=" C21 CTY A3201 " ideal model delta sigma weight residual 1.489 1.417 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C ASP C 230 " pdb=" N HIS C 231 " ideal model delta sigma weight residual 1.333 1.278 0.055 1.59e-02 3.96e+03 1.19e+01 bond pdb=" C26 CTY A3201 " pdb=" O9 CTY A3201 " ideal model delta sigma weight residual 1.480 1.548 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C18 CTY A3201 " pdb=" O4 CTY A3201 " ideal model delta sigma weight residual 1.481 1.548 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 103034 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.73: 17681 105.73 - 113.57: 63312 113.57 - 121.40: 47368 121.40 - 129.23: 23661 129.23 - 137.07: 3303 Bond angle restraints: 155325 Sorted by residual: angle pdb=" N ASP M 31 " pdb=" CA ASP M 31 " pdb=" C ASP M 31 " ideal model delta sigma weight residual 107.73 113.98 -6.25 1.34e+00 5.57e-01 2.18e+01 angle pdb=" C3' U A2447 " pdb=" O3' U A2447 " pdb=" P G A2448 " ideal model delta sigma weight residual 120.20 113.32 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C VAL Y 5 " pdb=" N SER Y 6 " pdb=" CA SER Y 6 " ideal model delta sigma weight residual 120.86 127.88 -7.02 1.60e+00 3.91e-01 1.93e+01 angle pdb=" C2' A A1109 " pdb=" C1' A A1109 " pdb=" N9 A A1109 " ideal model delta sigma weight residual 112.00 118.55 -6.55 1.50e+00 4.44e-01 1.91e+01 angle pdb=" C2' A A 856 " pdb=" C1' A A 856 " pdb=" N9 A A 856 " ideal model delta sigma weight residual 112.00 118.47 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 155320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 51084 35.99 - 71.97: 3050 71.97 - 107.96: 223 107.96 - 143.95: 18 143.95 - 179.94: 12 Dihedral angle restraints: 54387 sinusoidal: 45329 harmonic: 9058 Sorted by residual: dihedral pdb=" CA ARG W 73 " pdb=" C ARG W 73 " pdb=" N GLY W 74 " pdb=" CA GLY W 74 " ideal model delta harmonic sigma weight residual -180.00 -112.46 -67.54 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" O4' C A3060 " pdb=" C1' C A3060 " pdb=" N1 C A3060 " pdb=" C2 C A3060 " ideal model delta sinusoidal sigma weight residual 200.00 20.06 179.94 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual -160.00 18.64 -178.64 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 54384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.085: 19987 1.085 - 2.169: 0 2.169 - 3.254: 0 3.254 - 4.339: 0 4.339 - 5.424: 4 Chirality restraints: 19991 Sorted by residual: chirality pdb=" C16 CTY A3201 " pdb=" C15 CTY A3201 " pdb=" C17 CTY A3201 " pdb=" C19 CTY A3201 " both_signs ideal model delta sigma weight residual False 2.65 -2.77 5.42 2.00e-01 2.50e+01 7.35e+02 chirality pdb=" C6 CTY A3201 " pdb=" C32 CTY A3201 " pdb=" C5 CTY A3201 " pdb=" C7 CTY A3201 " both_signs ideal model delta sigma weight residual False -2.76 2.65 -5.40 2.00e-01 2.50e+01 7.30e+02 chirality pdb=" C12 CTY A3201 " pdb=" C11 CTY A3201 " pdb=" C13 CTY A3201 " pdb=" C35 CTY A3201 " both_signs ideal model delta sigma weight residual False -2.74 2.66 -5.40 2.00e-01 2.50e+01 7.29e+02 ... (remaining 19988 not shown) Planarity restraints: 7673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 856 " 0.059 2.00e-02 2.50e+03 2.65e-02 1.93e+01 pdb=" N9 A A 856 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A A 856 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A A 856 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A A 856 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 856 " 0.012 2.00e-02 2.50e+03 pdb=" N6 A A 856 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 856 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A 856 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A A 856 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A A 856 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1366 " 0.059 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" N9 G A1366 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G A1366 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A1366 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A1366 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A1366 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G A1366 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A1366 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A1366 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A1366 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A1366 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G A1366 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 104 " 0.050 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR E 104 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 104 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 104 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 104 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 104 " 0.017 2.00e-02 2.50e+03 ... (remaining 7670 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 1818 2.57 - 3.15: 75114 3.15 - 3.73: 188397 3.73 - 4.32: 265088 4.32 - 4.90: 360644 Nonbonded interactions: 891061 Sorted by model distance: nonbonded pdb=" OG1 THR V 15 " pdb=" OE1 GLU V 16 " model vdw 1.984 2.440 nonbonded pdb=" O2' G A 806 " pdb=" O2' G A2307 " model vdw 1.989 2.440 nonbonded pdb=" OG1 THR Z 7 " pdb=" OG SER Z 34 " model vdw 1.991 2.440 nonbonded pdb=" O2 U A1164 " pdb=" O6 G A1249 " model vdw 2.016 2.432 nonbonded pdb=" OP1 A A 856 " pdb=" O2' A A1669 " model vdw 2.017 2.440 ... (remaining 891056 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3234 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 46439 2.51 5 N 17748 2.21 5 O 26888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 15.550 Check model and map are aligned: 1.090 Convert atoms to be neutral: 0.600 Process input model: 352.840 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 376.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.009 0.130 103039 Z= 0.570 Angle : 1.043 12.266 155325 Z= 0.515 Chirality : 0.092 5.424 19991 Planarity : 0.007 0.074 7673 Dihedral : 17.882 179.935 48581 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 20.50 % Favored : 79.12 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.43 % 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: -5.56 (0.11), residues: 3156 helix: -3.13 (0.13), residues: 760 sheet: -3.59 (0.19), residues: 463 loop : -4.19 (0.10), residues: 1933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 586 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 604 average time/residue: 1.0688 time to fit residues: 1026.7132 Evaluate side-chains 481 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 460 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6481 time to fit residues: 30.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 532 optimal weight: 9.9990 chunk 478 optimal weight: 0.9980 chunk 265 optimal weight: 50.0000 chunk 163 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 494 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 573 optimal weight: 9.9990 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN 3 31 HIS ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 4 ASN C 113 GLN C 135 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS D 69 GLN D 99 GLN E 41 HIS E 47 GLN F 26 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 40 HIS J 130 HIS J 132 HIS ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN N 54 HIS N 62 ASN N 77 HIS O 45 GLN Q 39 GLN Q 66 ASN Q 72 ASN Q 94 ASN U 70 ASN V 44 HIS V 58 HIS V 82 HIS W 12 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 103039 Z= 0.231 Angle : 0.736 33.448 155325 Z= 0.364 Chirality : 0.047 2.191 19991 Planarity : 0.006 0.077 7673 Dihedral : 16.997 179.529 42418 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.18 % Favored : 86.69 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.50 (0.12), residues: 3156 helix: -1.89 (0.17), residues: 757 sheet: -3.04 (0.20), residues: 487 loop : -3.63 (0.11), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 505 time to evaluate : 4.013 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 62 residues processed: 560 average time/residue: 1.0285 time to fit residues: 962.6040 Evaluate side-chains 504 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 442 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.7010 time to fit residues: 85.7522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 0.2980 chunk 390 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 620 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 569 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 460 optimal weight: 8.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN E 140 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Q 72 ASN R 77 HIS W 12 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 103039 Z= 0.265 Angle : 0.734 27.728 155325 Z= 0.360 Chirality : 0.047 2.215 19991 Planarity : 0.006 0.057 7673 Dihedral : 16.783 178.998 42418 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.80 % Favored : 85.11 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.05 (0.13), residues: 3156 helix: -1.49 (0.17), residues: 762 sheet: -2.80 (0.20), residues: 485 loop : -3.34 (0.12), residues: 1909 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 474 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 58 residues processed: 549 average time/residue: 0.9462 time to fit residues: 863.1560 Evaluate side-chains 500 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 442 time to evaluate : 3.810 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 58 outliers final: 1 residues processed: 58 average time/residue: 0.6592 time to fit residues: 77.8347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 2.9990 chunk 431 optimal weight: 30.0000 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 576 optimal weight: 6.9990 chunk 609 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 546 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 44 GLN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN T 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 103039 Z= 0.353 Angle : 0.809 28.592 155325 Z= 0.395 Chirality : 0.050 2.153 19991 Planarity : 0.006 0.056 7673 Dihedral : 16.903 178.242 42418 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.06 % Favored : 83.84 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.13), residues: 3156 helix: -1.44 (0.17), residues: 761 sheet: -2.72 (0.21), residues: 476 loop : -3.26 (0.12), residues: 1919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 446 time to evaluate : 3.809 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 69 residues processed: 516 average time/residue: 0.9479 time to fit residues: 810.4160 Evaluate side-chains 504 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 435 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.6981 time to fit residues: 94.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 507 optimal weight: 3.9990 chunk 346 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 454 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 520 optimal weight: 30.0000 chunk 421 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 547 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 103039 Z= 0.273 Angle : 0.733 27.408 155325 Z= 0.360 Chirality : 0.047 2.151 19991 Planarity : 0.006 0.060 7673 Dihedral : 16.733 179.078 42418 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.99 % Favored : 84.92 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.13), residues: 3156 helix: -1.15 (0.18), residues: 758 sheet: -2.63 (0.21), residues: 484 loop : -3.12 (0.12), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 451 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 49 residues processed: 505 average time/residue: 0.9864 time to fit residues: 829.6322 Evaluate side-chains 482 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 433 time to evaluate : 3.829 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.6979 time to fit residues: 69.4048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 205 optimal weight: 10.0000 chunk 549 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 610 optimal weight: 5.9990 chunk 506 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 32 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 HIS ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 103039 Z= 0.397 Angle : 0.851 28.610 155325 Z= 0.414 Chirality : 0.052 2.149 19991 Planarity : 0.006 0.059 7673 Dihedral : 16.965 177.922 42418 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.86 % Favored : 83.05 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.13), residues: 3156 helix: -1.40 (0.17), residues: 759 sheet: -2.72 (0.21), residues: 490 loop : -3.14 (0.12), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 437 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 56 residues processed: 493 average time/residue: 1.0274 time to fit residues: 841.5045 Evaluate side-chains 477 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 421 time to evaluate : 3.851 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.7108 time to fit residues: 78.8674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 588 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 445 optimal weight: 30.0000 chunk 345 optimal weight: 20.0000 chunk 513 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 608 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 280 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 103039 Z= 0.377 Angle : 0.836 28.090 155325 Z= 0.407 Chirality : 0.051 2.148 19991 Planarity : 0.006 0.056 7673 Dihedral : 16.974 178.574 42418 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.29 % Favored : 83.62 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.13), residues: 3156 helix: -1.40 (0.17), residues: 760 sheet: -2.64 (0.21), residues: 478 loop : -3.12 (0.12), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 439 time to evaluate : 4.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 43 residues processed: 486 average time/residue: 0.9896 time to fit residues: 798.6799 Evaluate side-chains 470 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 427 time to evaluate : 3.911 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.7295 time to fit residues: 62.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 376 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 414 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 103039 Z= 0.344 Angle : 0.805 27.659 155325 Z= 0.393 Chirality : 0.050 2.146 19991 Planarity : 0.006 0.092 7673 Dihedral : 16.910 178.995 42418 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.19 % Favored : 83.71 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.13), residues: 3156 helix: -1.32 (0.17), residues: 759 sheet: -2.59 (0.21), residues: 490 loop : -3.05 (0.12), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 437 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 33 residues processed: 466 average time/residue: 0.9797 time to fit residues: 755.2982 Evaluate side-chains 459 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.6876 time to fit residues: 47.7179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 553 optimal weight: 2.9990 chunk 582 optimal weight: 8.9990 chunk 531 optimal weight: 5.9990 chunk 566 optimal weight: 5.9990 chunk 341 optimal weight: 30.0000 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 512 optimal weight: 2.9990 chunk 536 optimal weight: 9.9990 chunk 564 optimal weight: 0.0770 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 58 ASN J 135 GLN J 147 GLN L 6 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Q 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 103039 Z= 0.217 Angle : 0.682 26.550 155325 Z= 0.334 Chirality : 0.044 2.139 19991 Planarity : 0.005 0.060 7673 Dihedral : 16.502 179.880 42418 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.55 % Favored : 87.36 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.14), residues: 3156 helix: -0.93 (0.18), residues: 756 sheet: -2.45 (0.22), residues: 489 loop : -2.91 (0.13), residues: 1911 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 452 time to evaluate : 3.903 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 464 average time/residue: 1.0003 time to fit residues: 761.3461 Evaluate side-chains 431 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 420 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6797 time to fit residues: 18.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 372 optimal weight: 0.0570 chunk 599 optimal weight: 0.0010 chunk 365 optimal weight: 0.9990 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 30.0000 chunk 628 optimal weight: 2.9990 chunk 578 optimal weight: 4.9990 chunk 500 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 overall best weight: 0.8246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 3 63 ASN ** 6 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 HIS ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 103039 Z= 0.129 Angle : 0.594 26.896 155325 Z= 0.289 Chirality : 0.040 2.130 19991 Planarity : 0.005 0.057 7673 Dihedral : 15.877 179.711 42418 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.92 % Favored : 89.99 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 3156 helix: -0.36 (0.19), residues: 757 sheet: -2.11 (0.22), residues: 497 loop : -2.62 (0.13), residues: 1902 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 491 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 496 average time/residue: 1.0089 time to fit residues: 819.9963 Evaluate side-chains 443 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 438 time to evaluate : 3.814 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6739 time to fit residues: 10.3988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 397 optimal weight: 30.0000 chunk 533 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 461 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Q 77 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.165518 restraints weight = 139621.756| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.10 r_work: 0.3625 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 103039 Z= 0.367 Angle : 0.802 27.871 155325 Z= 0.389 Chirality : 0.049 2.128 19991 Planarity : 0.006 0.056 7673 Dihedral : 16.330 178.391 42418 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.61 % Favored : 85.30 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.14), residues: 3156 helix: -0.89 (0.18), residues: 756 sheet: -2.29 (0.21), residues: 498 loop : -2.76 (0.13), residues: 1902 =============================================================================== Job complete usr+sys time: 15157.10 seconds wall clock time: 272 minutes 25.44 seconds (16345.44 seconds total)