Starting phenix.real_space_refine on Fri Dec 15 21:16:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_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_2023/7f0d_31398_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/12_2023/7f0d_31398_updated.pdb" } resolution = 3.3 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= 0.000 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 63.06, per 1000 atoms: 0.67 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: 42.32 Conformation dependent library (CDL) restraints added in 3.9 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: 52.19 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: 152.45 Time building geometry restraints manager: 45.33 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=" C1 CTY A3201 " pdb=" O2 CTY A3201 " ideal model delta sigma weight residual 1.568 1.447 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C26 CTY A3201 " pdb=" C27 CTY A3201 " ideal model delta sigma weight residual 1.503 1.395 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C18 CTY A3201 " pdb=" C21 CTY A3201 " ideal model delta sigma weight residual 1.490 1.417 0.073 2.00e-02 2.50e+03 1.34e+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=" C11 CTY A3201 " pdb=" O12 CTY A3201 " ideal model delta sigma weight residual 1.341 1.408 -0.067 2.00e-02 2.50e+03 1.11e+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: 55594 35.99 - 71.97: 7470 71.97 - 107.96: 936 107.96 - 143.95: 29 143.95 - 179.94: 31 Dihedral angle restraints: 64060 sinusoidal: 55002 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 64057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.095: 19973 1.095 - 2.190: 0 2.190 - 3.285: 0 3.285 - 4.380: 0 4.380 - 5.475: 3 Chirality restraints: 19976 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 2.71 -2.77 5.48 2.00e-01 2.50e+01 7.49e+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 -2.76 2.66 -5.42 2.00e-01 2.50e+01 7.34e+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 -5.41 2.00e-01 2.50e+01 7.31e+02 ... (remaining 19973 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 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: 4.040 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: 0.090 Extract box with map and model: 13.220 Check model and map are aligned: 1.060 Set scattering table: 0.660 Process input model: 368.330 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.280 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 391.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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= 0.572 Angle : 1.043 12.266 155325 Z= 0.515 Chirality : 0.086 5.475 19976 Planarity : 0.007 0.074 7673 Dihedral : 24.667 179.935 58254 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 20.50 % Favored : 79.12 % Rotamer: Outliers : 1.00 % Allowed : 15.17 % Favored : 83.83 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 206 HIS 0.019 0.002 HIS 6 42 PHE 0.025 0.003 PHE 2 21 TYR 0.066 0.004 TYR E 104 ARG 0.021 0.001 ARG E 52 *********************** 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 : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 604 average time/residue: 1.1084 time to fit residues: 1061.5617 Evaluate side-chains 481 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 460 time to evaluate : 3.752 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6724 time to fit residues: 31.2304 ------------------------------------------------------------------------------- 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: 0.2980 chunk 265 optimal weight: 50.0000 chunk 163 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 0.9980 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: 3.6584 ------------------------------------------------------------------------------- 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 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** 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 M 17 GLN 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: 0.7232 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 103039 Z= 0.223 Angle : 0.728 29.649 155325 Z= 0.358 Chirality : 0.045 1.959 19976 Planarity : 0.006 0.074 7673 Dihedral : 24.664 179.949 52091 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.45 % Favored : 87.42 % Rotamer: Outliers : 3.62 % Allowed : 19.48 % Favored : 76.90 % 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: -4.44 (0.12), residues: 3156 helix: -1.83 (0.17), residues: 755 sheet: -3.01 (0.20), residues: 487 loop : -3.59 (0.11), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 250 HIS 0.011 0.001 HIS 6 42 PHE 0.017 0.002 PHE P 73 TYR 0.026 0.002 TYR J 125 ARG 0.013 0.001 ARG K 69 *********************** 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 599 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 505 time to evaluate : 3.734 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 59 residues processed: 562 average time/residue: 1.0150 time to fit residues: 943.9890 Evaluate side-chains 501 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 442 time to evaluate : 3.771 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.7309 time to fit residues: 85.0713 ------------------------------------------------------------------------------- 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: 2.9990 chunk 390 optimal weight: 0.4980 chunk 158 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 511 optimal weight: 10.0000 chunk 569 optimal weight: 0.9980 chunk 195 optimal weight: 20.0000 chunk 460 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 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 21 ASN E 140 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1282 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= 0.276 Angle : 0.744 27.621 155325 Z= 0.365 Chirality : 0.046 1.975 19976 Planarity : 0.006 0.058 7673 Dihedral : 24.523 179.641 52091 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.02 % Favored : 84.89 % Rotamer: Outliers : 3.74 % Allowed : 22.49 % Favored : 73.78 % 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: -4.07 (0.13), residues: 3156 helix: -1.52 (0.17), residues: 758 sheet: -2.83 (0.20), residues: 486 loop : -3.35 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 206 HIS 0.008 0.001 HIS 6 42 PHE 0.014 0.002 PHE 2 21 TYR 0.037 0.002 TYR E 104 ARG 0.009 0.001 ARG E 52 *********************** 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 571 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 474 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 56 residues processed: 540 average time/residue: 1.0022 time to fit residues: 895.4056 Evaluate side-chains 498 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 442 time to evaluate : 3.765 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.7427 time to fit residues: 82.3946 ------------------------------------------------------------------------------- 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: 6.9990 chunk 431 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 576 optimal weight: 3.9990 chunk 609 optimal weight: 0.9980 chunk 300 optimal weight: 10.0000 chunk 546 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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** ** 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 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** T 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 103039 Z= 0.301 Angle : 0.759 28.050 155325 Z= 0.371 Chirality : 0.047 1.960 19976 Planarity : 0.006 0.058 7673 Dihedral : 24.490 179.705 52091 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.86 % Favored : 85.04 % Rotamer: Outliers : 3.89 % Allowed : 24.37 % Favored : 71.74 % 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: -3.85 (0.13), residues: 3156 helix: -1.34 (0.17), residues: 759 sheet: -2.70 (0.21), residues: 483 loop : -3.20 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 48 HIS 0.008 0.001 HIS 6 42 PHE 0.014 0.002 PHE L 70 TYR 0.038 0.002 TYR E 104 ARG 0.010 0.001 ARG G 164 *********************** 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 551 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 450 time to evaluate : 3.726 Fit side-chains revert: symmetry clash outliers start: 101 outliers final: 65 residues processed: 521 average time/residue: 1.0599 time to fit residues: 923.9683 Evaluate side-chains 498 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 433 time to evaluate : 3.764 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.7746 time to fit residues: 99.3950 ------------------------------------------------------------------------------- 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: 7.9990 chunk 346 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 454 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 30.0000 chunk 421 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 547 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 overall best weight: 5.2986 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 103039 Z= 0.287 Angle : 0.743 28.192 155325 Z= 0.364 Chirality : 0.046 1.957 19976 Planarity : 0.006 0.050 7673 Dihedral : 24.446 179.808 52091 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.15 % Favored : 84.76 % Rotamer: Outliers : 2.81 % Allowed : 26.80 % Favored : 70.39 % 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: -3.70 (0.13), residues: 3156 helix: -1.19 (0.18), residues: 759 sheet: -2.62 (0.21), residues: 484 loop : -3.11 (0.12), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 48 HIS 0.007 0.001 HIS Q 41 PHE 0.015 0.002 PHE G 91 TYR 0.026 0.002 TYR J 125 ARG 0.007 0.001 ARG W 39 *********************** 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 526 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 453 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 39 residues processed: 499 average time/residue: 1.0091 time to fit residues: 830.7966 Evaluate side-chains 476 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 437 time to evaluate : 3.768 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.6881 time to fit residues: 55.6856 ------------------------------------------------------------------------------- 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: 0.8980 chunk 282 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 overall best weight: 6.9792 ------------------------------------------------------------------------------- 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** 4 32 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS E 127 ASN ** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 103039 Z= 0.360 Angle : 0.815 27.893 155325 Z= 0.397 Chirality : 0.049 1.952 19976 Planarity : 0.006 0.075 7673 Dihedral : 24.502 179.723 52091 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.22 % Favored : 83.68 % Rotamer: Outliers : 3.39 % Allowed : 27.96 % Favored : 68.66 % 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: -3.76 (0.13), residues: 3156 helix: -1.29 (0.17), residues: 758 sheet: -2.68 (0.21), residues: 499 loop : -3.10 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 206 HIS 0.009 0.002 HIS Q 41 PHE 0.025 0.003 PHE G 91 TYR 0.027 0.002 TYR E 104 ARG 0.009 0.001 ARG C 157 *********************** 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 532 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 444 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 56 residues processed: 498 average time/residue: 1.0248 time to fit residues: 843.3339 Evaluate side-chains 484 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 428 time to evaluate : 4.425 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.7038 time to fit residues: 79.7792 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 445 optimal weight: 7.9990 chunk 345 optimal weight: 20.0000 chunk 513 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 608 optimal weight: 8.9990 chunk 380 optimal weight: 4.9990 chunk 370 optimal weight: 0.4980 chunk 280 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** 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 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 103039 Z= 0.304 Angle : 0.763 27.933 155325 Z= 0.373 Chirality : 0.047 1.952 19976 Planarity : 0.006 0.053 7673 Dihedral : 24.460 179.959 52091 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.02 % Favored : 84.85 % Rotamer: Outliers : 2.62 % Allowed : 28.22 % Favored : 69.16 % 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: -3.60 (0.13), residues: 3156 helix: -1.19 (0.18), residues: 763 sheet: -2.52 (0.22), residues: 479 loop : -3.02 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 48 HIS 0.008 0.001 HIS Q 41 PHE 0.023 0.002 PHE G 91 TYR 0.023 0.002 TYR J 125 ARG 0.010 0.001 ARG W 39 *********************** 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 508 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 440 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 485 average time/residue: 1.0930 time to fit residues: 884.7366 Evaluate side-chains 466 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 427 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7429 time to fit residues: 59.1454 ------------------------------------------------------------------------------- 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: 10.0000 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 478 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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** ** 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 127 ASN ** 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 H 44 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** ** 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: 0.7325 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 103039 Z= 0.407 Angle : 0.865 27.427 155325 Z= 0.420 Chirality : 0.051 1.948 19976 Planarity : 0.007 0.057 7673 Dihedral : 24.547 179.219 52091 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.05 % Favored : 82.86 % Rotamer: Outliers : 2.27 % Allowed : 29.07 % Favored : 68.66 % 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: -3.77 (0.13), residues: 3156 helix: -1.41 (0.17), residues: 763 sheet: -2.61 (0.22), residues: 476 loop : -3.10 (0.12), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 206 HIS 0.010 0.002 HIS Q 41 PHE 0.024 0.003 PHE 2 8 TYR 0.029 0.003 TYR E 104 ARG 0.010 0.001 ARG W 39 *********************** 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 503 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 444 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 477 average time/residue: 1.0244 time to fit residues: 807.8738 Evaluate side-chains 464 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 431 time to evaluate : 3.898 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7326 time to fit residues: 50.2453 ------------------------------------------------------------------------------- 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: 6.9990 chunk 582 optimal weight: 0.0570 chunk 531 optimal weight: 6.9990 chunk 566 optimal weight: 0.9980 chunk 341 optimal weight: 30.0000 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 512 optimal weight: 6.9990 chunk 536 optimal weight: 0.4980 chunk 564 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN ** 6 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN J 58 ASN L 6 HIS ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN V 7 ASN V 38 HIS ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 103039 Z= 0.143 Angle : 0.637 28.384 155325 Z= 0.312 Chirality : 0.041 1.971 19976 Planarity : 0.005 0.052 7673 Dihedral : 24.216 178.820 52091 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.61 % Rotamer: Outliers : 0.73 % Allowed : 29.65 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.14 (0.14), residues: 3156 helix: -0.73 (0.18), residues: 768 sheet: -2.20 (0.22), residues: 494 loop : -2.76 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 250 HIS 0.009 0.001 HIS C 143 PHE 0.017 0.002 PHE 2 8 TYR 0.025 0.002 TYR C 104 ARG 0.020 0.001 ARG C 91 *********************** 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 505 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 486 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 498 average time/residue: 1.0679 time to fit residues: 867.8391 Evaluate side-chains 447 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 440 time to evaluate : 3.748 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6995 time to fit residues: 13.3938 ------------------------------------------------------------------------------- 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: 4.9990 chunk 599 optimal weight: 0.5980 chunk 365 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 30.0000 chunk 628 optimal weight: 6.9990 chunk 578 optimal weight: 5.9990 chunk 500 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 3 53 ASN ** 6 42 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** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN L 106 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 103039 Z= 0.181 Angle : 0.632 28.357 155325 Z= 0.308 Chirality : 0.041 1.960 19976 Planarity : 0.005 0.074 7673 Dihedral : 24.087 179.847 52091 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.76 % Favored : 88.15 % Rotamer: Outliers : 0.19 % Allowed : 31.00 % Favored : 68.81 % 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: -3.01 (0.14), residues: 3156 helix: -0.59 (0.18), residues: 768 sheet: -2.14 (0.22), residues: 500 loop : -2.70 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 65 HIS 0.007 0.001 HIS C 143 PHE 0.018 0.002 PHE 2 8 TYR 0.020 0.002 TYR D 54 ARG 0.014 0.001 ARG C 157 ********************** 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 448 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 443 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 445 average time/residue: 1.0616 time to fit residues: 773.5889 Evaluate side-chains 439 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 434 time to evaluate : 3.729 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6935 time to fit residues: 10.6228 ------------------------------------------------------------------------------- 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: 0.9990 chunk 153 optimal weight: 10.0000 chunk 461 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 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** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.166558 restraints weight = 139209.458| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.01 r_work: 0.3647 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 0.005 0.067 103039 Z= 0.296 Angle : 0.734 28.590 155325 Z= 0.357 Chirality : 0.046 1.947 19976 Planarity : 0.006 0.085 7673 Dihedral : 24.183 179.933 52091 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.23 % Favored : 85.68 % Rotamer: Outliers : 0.77 % Allowed : 30.73 % Favored : 68.50 % 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: -3.18 (0.14), residues: 3156 helix: -0.82 (0.18), residues: 768 sheet: -2.25 (0.22), residues: 495 loop : -2.76 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 65 HIS 0.007 0.001 HIS Q 41 PHE 0.024 0.002 PHE L 49 TYR 0.035 0.002 TYR C 104 ARG 0.016 0.001 ARG 1 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16228.87 seconds wall clock time: 291 minutes 25.86 seconds (17485.86 seconds total)